Lieutenant General Thomas Metz, the second most senior American officer in Iraq and the force's tactical operations commander, said the US military was prepared to risk provoking "friction" with the new government in strikes against "professional terrorists".

His frank admission, just two days after sovereignty was handed back to the Iraqis, cuts to the heart of a likely source of significant political disagreement between the fledgling government and the US military in the near future.

"I think there will be judgment calls, and a major part of the equation will be how does it impact our partnership with the Iraqis? If the independent strike causes too much friction and rift in the partnership, then we may choose not to do it. If it is so valuable to the global war on terrorism to make this strike, then we may choose to accept the friction and temporary disagreement because of the value of it," said Gen Metz.

In particular, he said that if the target was Abu Musab al-Zarqawi, the Jordanian militant blamed for the most violent attacks in Iraq, or one of his followers, the strike would go ahead, possibly before the Iraqi government was told.

"I personally believe that with Zarqawi in my sights I've got to pull the trigger, not only to the benefit of the Iraqis and their sovereignty, but also [to] the global war on terrorism."

All coalition commanders in Iraq, including the British, report to Gen Metz, a West Point graduate, 56, who talks with a North Carolina drawl. He is deputy to George Casey, the first four-star general deployed in Iraq, who takes command today, and works in an office overlooking the lake at what was once Saddam Hussein's al-Faw palace, near Baghdad airport.

The general spoke of a shift in approach to military operations in Iraq. Rather than focusing on "intelligence-based operations", his men would now concentrate on protecting the new Iraqi government and its infrastructure, and work to develop the Iraqi police, the national guard and the military, he said.

The new prime minister, Ayad Allawi, has already suggested he is planning a tough security policy, including a state of emergency with curfews and detentions.

Gen Metz said US troops would avoid enforcing such a politically sensitive crackdown. "I would envision the coalition forces probably in the quick-reaction role, as opposed to walking the beat to ensure a curfew or whatever they have asked us to do," he said.

But he acknowledged that the Iraqi security forces, still under-equipped and undertrained 15 months after the war, were a long way from taking charge of policing their country. It would be autumn before they would be able to provide security in most areas of Iraq. "It will be September [to] October before we can look at lots of places across the country being at local control," he said. In particular, in western Iraq, the scene of much of the insurgency, the Iraqi forces were least prepared, he said.

He acknowledged that the violent insurgency, which has already claimed the lives of more than 600 American troops and more than 500 Iraqi police, was not likely to end, although he believed that Iraqis would eventually be able to fight it alone.

"My opinion is you may never get to a zero insurgency in Iraq," he said. "I think there is enough turmoil in this part of the world that there will be some element out there that will be opposed to the government and will be violent and lethal."

He offered a rarely-voiced analysis of the Iraqi resistance, saying he believed that divisions would emerge eventually between Islamists from the Zarqawi network, who would want to set up a religious, hardline "caliphate of the next generation" across the Middle East, and remnants of Saddam Hussein's regime, who wanted a return to power in Baghdad.

"Because their long-term goals are so different, they won't stay together very long," he said. He said that the Zarqawi group wanted to remain independent from Osama bin Laden or al-Qaida, although it shared their goal.

The general admitted that foreign fighters, who are routinely blamed by US political leaders for most of the attacks, in fact represented less than a quarter of the insurgents, though they were better trained and more lethal.

Although he said he believed that security would be good enough to permit elections to be held as scheduled next January, he warned that it would not be easy. "It is going to be a lot of hard work to get us there," he said.