The relationship is crucial to American plans to start withdrawing troops from Afghanistan next year.
Washington has kept up pressure on Islamabad to launch a ground offensive against militant bases in North Waziristan.
And Pakistan is also the most important route for channelling supplies to the Nato-led force.
However, American diplomats say they are facing increased levels of harassment and have seen a slow-down in visas being issued.
Husain Haqqani, Pakistani ambassador to Washington, said: “The CIA and ISI are working through some issues.” via telegraph.co.uk