Afghanistan-Pakistan: The Covert War
Image Credit: REUTERS/Parwiz

Afghanistan-Pakistan: The Covert War


When American special forces plucked the second in command of the Pakistani Taliban from the hands of Afghan officials this October, they laid bare the extent of a largely covert war between Afghanistan and Pakistan that has been going on for several years. With a drawdown – perhaps even to zero – of U.S. troops from Afghanistan next year, the secret war might just become an open one.

The capture of Latif Mehsud proved to be an embarrassment for the Afghans, and a vindication for Pakistan, which has long complained that the Pakistani Taliban – called the Tehrik -e-Taliban (TTP) – receives support from Karzai’s government. Afghanistan and the United States, for their part, have laid the blame for a 12-year insurgency at Pakistan’s feet, saying its intelligence agencies support the most effective insurgency group, led by Jalaluddin Haqqani.

Latif Mehsud was a close confidant of Qari Hussain, who was one of the candidates to take over the TTP after the killing of its leader, Baitullah Mehsud, by an American drone strike in 2009. When Hussain was similarly eliminated in October 2010, Latif took over as the TTP’s second in command, operating under its leader, Hakimullah Mehsud. (The two Mehsuds are from the same tribe, but not closely related.) Latif’s capture provided the intelligence the U.S. needed to kill Hakimullah, in a drone strike just a few weeks later.

Latif spent much of his time since 2010 between Afghanistan and Pakistan, and it is believed he was a conduit for funding to the TTP. It now appears some of that funding might have come from Afghanistan’s intelligence agency, the National Directorate of Security (NDS).

On October 5, Latif was being taken by Afghan officials to a meeting with agents from the NDS when American special forces stopped his convoy, taking Latif to Bagram, where the U.S. runs a prison of its own.

The TTP has been blamed for tens of thousands of deaths in Pakistan, in brazen attacks on government and civilian targets alike that began in 2007. The group has also claimed responsibility for an attempted car bombing in New York City in 2010.

It’s not the kind of group Karzai’s government would ostensibly want to be associated with.

Yet, the president’s spokesperson, Aimal Faizi, openly told reporters the NDS had been working with Latif “for a long period of time.” Latif, Faizi said, “was part of an NDS project like every other intelligence agency is doing.”

The Afghans evidently decided it was time to cultivate their own proxies for leverage with Pakistan.

The Haqqani insurgent network, which has inflicted the most damage on Afghan and U.S. forces, is based in North Waziristan, where Pakistan has thousands of troops stationed, but has held off on trying to clear the area of militants. It is also home to a number of senior TTP members, and has borne the brunt of American drone strikes.

“The Haqqani network…acts as a veritable arm of Pakistan’s Inter-Services Intelligence Agency,” Admiral Mike Mullen, the then top American military official told Congress in 2011. U.S. officials were irate, saying as far back as 2008, they had tracked the communication lines of Haqqani militants during attacks in Kabul to control rooms in Pakistan, which was directing the operation in real time. None of the evidence was made public, but the NDS was apparently motivated to offer funding to the TTP through operatives like Latif Mehsud. The TTP has a stated goal of toppling the Pakistani state, just as the Afghan Taliban hope to topple the Karzai government.

There is also speculation the NDS might be carrying out an assassination program of its own in Pakistan. In an embarrassing development for Pakistan, a gunman shot dead Nasiruddin Haqqani, a top facilitator of the insurgent group, in the Pakistani capitol of Islamabad last month.

Both the Afghan Taliban and the TTP operate across the Afghanistan-Pakistan border, each country turning a blind eye to their presence. When top leadership has been detained, they have been kept as bargaining chips instead of being extradited.

In 2009, Pakistan sent troops into the Swat Valley in a bid to retake control from Taliban-allied militants there. Within months, it claimed victory, but the militants’ leadership, including the group’s head Maulana Fazlullah, had escaped, making their way through Dir and across the border to Kunar.

When a drone strike killed the TTP’s head, Hakimullah Mehsud, this November, Fazlullah took his place. He has since made several trips to Pakistan, attending TTP meetings in North Waziristan, but is thought to still have safe-houses in Kunar.

Pakistan, which would like to negotiate a peace deal with the TTP, needs to get access to Fazlullah, but the key middle man is sitting in an NDS prison in Afghanistan.

Maulvi Faqir Muhammad was one of the founding members of the TTP, and commanded a force of more than six thousand fighters – Pakistanis, Afghans, and Arabs – in his native Bajaur Agency. When Pakistani troops flushed militants out of Bajaur in 2010, Faqir moved across the border into Afghanistan.

Faqir had a falling out with TTP leadership last year, when he openly called for negotiations with the Pakistani government. But he was reinstated soon after, at the behest of Fazlullah, and it is thought Faqir could help persuade the TTP head to consider peace talks. Or, if things don’t work out, Faqir could help locate Fazlullah so Pakistan, or maybe a U.S. drone strike, could take him out.

Getting to Fazlullah means getting at Faqir, much like finding Hakimullah Mehsud needed the cooperation of Latif Mehsud, who reportedly provided the intelligence used to locate the TTP’s former leader.

This February, Faqir was arrested by Afghan intelligence agents, and Karzai’s government has refused to extradite him to Pakistan. Afghan officials have said they are unwilling to do so until Pakistan hands over senior Taliban leaders in its custody like Mullah Baradar. Baradar was once the second in command of the Afghan Taliban, and is the natural point of contact for initiating peace talks between the insurgents and the Afghan government. Pakistan released him from prison in September, but only recently allowed Afghan negotiators limited access to him.

So each country now controls access to key militant leaders that could be used to influence the insurgency plaguing its rival.

Even as the covert war between Afghanistan and Pakistan continues, real skirmishes at the border have seen a dramatic rise over the last few years, foreshadowing the kind of tensions that might arise after coalition forces withdraw.

Pakistan and Afghanistan maintain more than a thousand border posts along the disputed, largely unmarked 2,600 kilometer border, but militants still move across with apparently little difficulty.

Pakistani forces have been known to, at the very least, ignore Haqqani network militants launching attacks into Afghanistan, but officials have also long accused the Afghans of doing the same thing.

In 2010, U.S. troops pulled out of strategic areas along the border like the Korengal Valley, redeploying to urban centers to protect the population from the Taliban insurgency. The move left a hole in the border, allowing for militants based in Kunar to strike targets in Pakistan.

In August, 2011, more than three hundred TTP fighters – Afghans and Pakistanis – crossed the border into Pakistan’s Chitral region, carrying out assaults on seven security posts over the course of several days, killing 32 Pakistani security personnel.

Two months later, more than two hundred fighters crossed into Pakistan’s Upper Dir area, sparking clashes that left one Pakistani soldier and 30 militants dead.

In neighboring Bajaur Agency, which Pakistan says it had cleared of militants by 2010, groups of up to 300 militants crossed over from Afghanistan during the summer of 2011 on three separate occasions, attacking government security posts and sparking clashes that lasted several days.

The raids have continued unabated in the last two years. In an effort to pursue the fighters, Pakistan routinely shells Afghanistan, often drawing retaliatory shelling by the Afghan National Army, which also fires at insurgents fleeing its own forces. Between the raids and the shelling, there has been a dramatic rise in casualties in the region: in 2009, 15 people were killed in cross-border violence, by 2012 the number of dead had reached 314.

If U.S. troops leave a vacuum in Afghanistan that the Haqqani insurgents begin to exploit, the Afghans are going to want leverage to force Pakistan to crack down on sanctuaries in its territory, and it seems that leverage will be the TTP. If the TTP’s insurgency in Pakistan picks up and the group’s leadership is still operating out of Afghanistan, there will be intense pressure on the Pakistanis to take military action – perhaps even a ground incursion – across the border.

Unless the Taliban on both sides of the border are pacified – either politically or militarily – before the U.S. withdrawal, the cross-border skirmishes could turn into an all-out war.

Umar Farooq is based in Pakistan, where he works as a correspondent for the Christian Science Monitor and the Wall Street Journal. He has also written for The Atlantic, Foreign Policy, The Globe and Mail, and The Nation.

January 3, 2014 at 20:44

When the USA leaves so will the brutal terror arm of the CIA namely blackwater ( whatever they are called today).

With US gone the chicken bleep bleep Indians will scurry and pack up their consulates.

This will be the end of TTP support and funding in Afghanistan and these TTP fighters will whither away or be killed.

Pashtuns hate the TTP in Pakistan And there are more Pashtuns in Pakistan than in Afghanistan.

Afghan Taliban is definitely going to return and to be honest Afghans would rather have them back then a vile bloody occupation led by USA.

As for India, your inflated ego on being a regional power let alone super power will pop. As for Pakistan it needs to take a hard look inwards and see where it has failed and look to its past to see where it was stronger.

As for India and Pak relations this will never improve and why should they while India continues to occupy lands of the Muslim Indus. The British have left a very deep hatred between the 2 groups and contrary to the inaccurate popular consensus it is more prevalent amongst the Hindus of India.

India has spread terror to all her neighbours and the wider region not just Pakistan. The West under the neocons just put a positive spin on India when in fact it is a treacherous cesspit of a nation.

January 4, 2014 at 07:05

@ Amin,
For you Pakis … the world would be simple once the Americans would be gone in 2014 …. but only in a world of denial that you Pakis live in … why do you Pakis think that funding for TTP will dry out, when funding for Paki strategic assets never end … ?? … India might close down its consulates if needed, but Indian influence will never end with the Afghans, that are historically friendly towards India, and India is committed to help them … and whether or not Afghanistan falls back into civil war post 2014, Pakistan is doomed either way …. and with reference to your take on India Pakistan relations, the people of India are in no rush for a better relations with you Pakis …

S. Suchindranath Aiyer
January 2, 2014 at 20:46

All this is very well, but, once the US cuts and runs from Afghanistan, it will relapse into an emirate providing “strategic depth” to that Saudi-Wahabi sword arm with the Islamic Bomb that will license its old ally China to loot the minerals to mutual profit:

January 3, 2014 at 21:05

Oh please stop creating bogey men.
Afghanistan would embrace the Taliban as opposed to the carnage caused by USA and her allies.

Hoping Afghanistanis and the majority Pashtuns will be smart enough to not get sucked into a Sunni v Shia struggle between Saudi and Iran but even that would be a blessing compared to the death destruction left by the USA led invasion.

Pashtuns must assert their own will on Afghanistan and in the same breath need to be weary of Indian games and hegemonic designs.

On Pakistan it is to be noted the Durand Line has never been recognised and more Pashtuns reside inside Pakistan than in Afghanistan. Pashtuns are the majority in Afghanistan so Pakistan will forever be joined with the destiny of Afghanistan whether people like it or not.

It is other powers regional and further away seeking to play the great game that is the problem and to be fair not Pakistan.

Had it not been Pakistani sacrifice and support the Afghanistan would be a Soviet / communist emirate today. Remember Pakistan was engaged in training and supporting the Mujahadeen way before the USA joined the cause. USA joined in the mid 80′s while Pakistan was working and supporting Afghan resistance from 1979.

Yes Pakistan must be wise too on how it spreads it’s influence or ideas into Afghanistan just like the new era of Taliban in Afghanistan.

Why not help the legitimate forces inside Afghanistan to recreate the rich and beautiful Afghanistan of the 50′s the centre of the world, cultural exchanges where East Is on the road to meet the West and visa vi.

For those powers seeking to continue the great game just remember Pashtuns and Afghans altogether are a tough bunch so stay clear or a insurgent highly militant Afghanistan will re emerge again.

January 2, 2014 at 16:58

There will not be a Pakistan-Afghanistan conflict. Saudi war lords will keep both happy. Instead their combined thrust will be against India – the regional exception.

After the Russians left until 2000 Pakistan enjoyed democracy for a change. That was when Taliban and Mujahiddin were running the show in Afghanistan.

January 3, 2014 at 20:56

To be fair the Taliban began as a movement to counter the Uzbek and Tajik warlords massacring the majority Pashtuns.

Who supported, armed and funded the Northerm Alliance violence against Pashtuns well it was India and Iran.

Iran now has different agenda but India continue to support those cold blooded killers funding them to remain in politics.

So pleaaaase enough of the BS please.

January 3, 2014 at 21:07


Even if it were true then Saudi has an important role across the Muslim world and would be a darn better scenario than the present for Afghans.

Do not treat Afghans like cattle mate…

They are a proud, strong and immensely beautiful people.

January 2, 2014 at 00:47

It has been known to all parties for many years, that there is a covert war going on in the Af-Pak region between Pakistan and Afghanistan. The BIG QUESTION here is, on whose side the US State Dept. and the CIA are ….
1. It has been apparent for quite some time now, that the American strategic objective post 2014, is in alignment with their major non-NATO ally Pakistan. The reason for that is simple. Pakistan is the only country, and a reliable proxy of the western powers in the region, that would their bidding in exchange of dollars … just as they did against the Soviets …
2. The well being of Afghanistan is not a priority of the Americans. The maneuver pattern of the Americans, and their definition of terrorist in their negotiation with the Afghans for a BSA treaty reveals that the Americans would, at any cost, protect the strategic interests of Pakistan, before their exit.
3. The American game plans for the region is not a secret any more. The countries in the region have their task cut out, to foil the American designs, in order to protect their own strategic and security interests, post 2014 ….

January 3, 2014 at 21:10

Deeply flawed narrative, Pakistan was already engaged in Afghan and Soviet war way before the US ever joined.

Pashtuns live on both sides of the Durand Line, family and blood is stronger than British made demarcation lines.

More Pashtuns exist in Pakistan today than Afghanistan therefore Pakistan is linked with Afghanistan by blood today, by ethnicity, by history, by geography, by religion and you can never change that but embrace it.

Learn the history of this region before the British and do not talk mambo jumbo..

January 4, 2014 at 06:49

@ Amin…
You Pakis are accomplished liars … With whose money and support was Pakistan engaged against the Soviets ( even before the US joined) … ??
Yeh … this narrative will always look flawed from a Pakistani point of view … because you Pakistanis think you are the only smart, and others are idiots …

January 4, 2014 at 07:11

I don’t need to learn history from a Paki … nor from the lie laden history books of Pakiland … ask any Afghan and he will confirm how much the Afghans hate you Pakis, it is historical, and for the same reason the Afghans love the people of India … who are you trying to bull shit here … ??

9 dashes, 4 dishes, 1 soup
January 1, 2014 at 21:24

Not that it matters, but I have predicted in posts on this publication for two years at least, the Taliban will turn its guns on the Pakistani government when NATO leaves.

If you view the Taliban as a Pashtun quasi-nationalist movement, there is no other conclusion to draw. Pakistan should dread the day when Americans are gone. It will either lose territory or thousands of its soldiers will die defending it – probably both.

January 3, 2014 at 20:53

On the contrary, with USA gone the tail that is India will not be too far behind.

TTP is not fighting the Afghan cause and nor is it an ideological struggle but of terror and incitement. With their financiers gone in Afghanistan the incompetent Afghan army will be incapable of protecting and financing them, agreed they will to begin with BUT we all know who the real power in Afghanistan are and that is Afghan Taliban.

The region will be a lot more stable with USA and India gone even if Afghanistan falls under the Emirate again. Offcourse India will whinge and whine because that’s what it does best but this will be a new era and there will be NO More neocon influence marketing the Indians.

Indians occupy land belonging to all its neighbours and have lived in an over inflated bubble that they are highly intelligent and progressive this last decade supported by the Zionist media people across the world have come to believe this until they visit the cess pit that is called India.

So do not worry about Pakistan, somebody quite accurately described it as a tough country and will go through some bumps before stability is restored.

Share your thoughts

Your Name
Your Email
required, but not published
Your Comment

Sign up for our weekly newsletter
The Diplomat Brief