Cardinal Keith O’Brien accused the Foreign Secretary of doubling overseas aid to Pakistan to more than £445 million without demanding religious freedom for Christians and other religious minorities, such as Shia Muslims.
He claimed that three-quarters of all religious persecution in the world is now directed at Christians, resulting in a collapse in the number of followers in some Middle East countries.
The cardinal was speaking ahead of the launch of a report into Christian persecution, which suggests it is getting worse in 22 of 34 ‘problem’ countries identified.
Earlier this month, Shahbaz Bhatti, the only Christian in the Pakistani government's cabinet, was shot dead by gunmen in Islamabad. He had previously spoken out against Pakistan's blasphemy laws.
Cardinal O’Brien, the head of the Catholic Church in Scotland, said: “I urge William Hague to obtain guarantees from foreign governments before they are given aid.
“To increase aid to the Pakistan government when religious freedom is not upheld and those who speak up for religious freedom are gunned down is tantamount to an anti-Christian foreign policy.
“This reality is both shocking and saddening. In countries like Afghanistan, Pakistan and Iraq, Christians face violence, intolerance and even death because of their beliefs.”
He said Mr Hague must put pressure on the governments of Pakistan and other Arab countries and make clear the provision of aid “must require a commitment to human rights.”
The report has been produced by Aid to the Church in Need, a Vatican-approved agency that helps persecuted Christians.
The situation is getting worse in two-thirds of the countries where the problem is most severe, the document found.
Over the past two years there have been more reports, or more severe examples, of violence and intimidation against Christians. These include attacks on churches and homes, kidnaps and killings.
Specific instances include a car bomb set off in January outside an Orthodox Church in Alexandria, Egypt, which killed more than 20 worshippers and wounded at least 70.
Asia Bibi, a Christian mother of five, was sentenced to death for blasphemy at the end of last year in the Punjab province of Pakistan. A mob had previously raided her home and beaten her.
The report found that in some parts of the Middle East the problem is so serious that it is uncertain whether Christianity “will survive another generation”.
In Iraq, the Christian population has fallen from 800,000 in 2002 to 150,000 now, while in neighbouring Iran it is “ebbing away into obscurity”.
The study blamed extreme Islamists in the Middle East, North Africa and Asia for targeting Christians, but also linked the dwindling numbers to a rise in nationalism in India, Sri Lanka and Burma.
Communist and atheistic states, such as Hugo Chavez’s Venezuela, were also accused of intimidating Christian groups.
Among the other countries where the report claimed Christian persecution is getting worse are China, Turkey, North Korea and Nigeria.
Alistair Burt, a Foreign Office Minister, said he shared the cardinal's concerns about Christians being persecuted but insisted religious freedom "is at the heart" of the UK's foreign policy.
“Britain raises concerns about religious freedom wherever they arise, including in Pakistan, through the intervention of ministers or our embassies and High Commissions," he said.
"We lobby governments about individual cases where persecution or discrimination occurs, and call for changes in discriminatory practices and laws in countries where freedom of religion is curtailed."
