“With Pakistan you have good cooperation in the counter-terrorism area and very legitimate concerns in others,” said a US counter-terrorism official knowledgeable about US ties with the ISI. “The Pakistani government, and the ISI in particular, are not monolithic. But the concerns we do have are well-founded and they have certainly not abated.”

Pakistani officials have repeatedly denied the allegation of ISI support for the Taliban.

Pakistani Prime Minister Yousaf Raza Gillani met with President George W Bush in Washington this week, with both leaders seeking to ease bilateral tensions over the conduct of the campaign against terrorism. Their talks focused on efforts to clamp down on al-Qaeda and Taliban extremists in Pakistan’s northwest tribal areas.

Gillani secured a pledge from Bush to respect Pakistani sovereignty in exchange for promises from Islamabad to crack down on the militants.

“This is our own war,” Gillani said. “This is a war which is against Pakistan.”

The four-month old coalition government in Islamabad has emphasised negotiations with militants and has characterised military action as a last resort. Pakistan, which has received more than $10 billion in US aid since 2001, has resisted suggestions that troops from the United States or other countries be allowed into the region.