While the two countries will continue to share vital intelligence about any imminent acts of terrorism, joint operations have been put on hold, the source said, and the ISI -- Pakistan's intelligence agency -- has asked the CIA to "give them visibility" over what the source says are an estimated 40 covert American intelligence operatives working in Pakistan.
The freeze brings U.S.-Pakistani intelligence cooperation to a new low. The two countries are already on rocky ground as Washington tries to persuade Islamabad of the need to allow it to autonomously hunt al Qaeda targets inside Pakistani territory. This has largely been conducted through unmanned aerial drone strikes -- another sore spot in relations, after such strikes have killed dozens of civilians.
The strained relationship dominated what one official called a "frank discussion" -- diplomatic jargon for a talk in which disagreements are aired openly -- Monday in Washington between CIA Director Leon Panetta and the chief of Pakistan's Inter Services Intelligence (ISI), Lt. Gen. Ahmad Shuja Pasha.
CIA spokesman Preston Golson called the meeting between the two men "productive" and said the "CIA-ISI relationship remains on solid footing."
One U.S. official referred to Pakistan as "playing a public negotiations versus private negotiations game," but the official said it is a "challenging situation," and the two nations are "working through differences."
"The bottom line is that joint cooperation is essential to the security of the two nations. The stakes are too high," said the official.
A U.S. official who is not authorized to speak on the record said, "Pakistan has asked for certain things and we're working it out," but the official would not elaborate.