The feeling is often mutual, which is why the CIA did not tell the ISI it had been tracking bin Laden in Abbottabad since last fall out of fear its cover would be blown. The recently departed station chief helped create that lack of trust by overseeing the intelligence gathering that led to Osama bin Laden's death, which included a network of undeclared Pakistani agents. Pakistani officials rounded up at least five Pakistanis accused of helping the CIA launch the Abbottabad raid, although only one remains in custody.
In Pakistan, the CIA station chief was reviled for his role in the raid, but in Washington, according to one official, he was widely praised. He "had the agency's full confidence," one U.S. official said.
The tension with the ISI began shortly after the recently departed station chief arrived. He helped try to release Raymond Davis, a CIA contractor who shot dead two men who Pakistani officials admit were working for the ISI. Davis told U.S. officials and Pakistani police that he shot the men believing he was being robbed by armed Pakistanis.
But the tension seems to also have been a product of a personality clash. A senior U.S. official who used to serve in Islamabad criticized the just departed station chief for not working hard enough to develop personal relationships with his Pakistani counterparts. Their relationship, the senior official said, was much worse than the relationship with the previous station chief as well the relationship cultivated by Vice Adm. Michael LeFever, who only recently departed as the top U.S. military officer in Pakistan.
U.S. officials declined to provide details about the station chief's illness.
The CIA declined to comment for this story.
Bad Marriage vs. Divorce
Recently, there have been some small signs of a thaw between the two agencies. The ISI granted 87 visas for CIA officers, bringing the CIA back to full strength in Pakistan, according to a Pakistani official. The official also said the U.S. and Pakistan agreed on a handful of "major" issues during a recent meeting between ISI Director Lt. Gen. Ahmad Shuja Pasha and acting CIA director Michael Morell, although the official would not provide details.
"The freefall has been arrested," said one Pakistani official close to the military.
But a U.S. official complained those visas were not good enough, since they were single entry and only valid for a few months. A separate, senior U.S. official said some of the visas were issued to officers who are no longer working in Pakistan.
The two agencies are far from recovering even the tense relationship they had late last year, when the previous station chief was outed, according to two Pakistani officials, in response to a court case filed in Brooklyn naming Pasha as a defendant.
But both sides say they are trying to work through the current tension.
"A bad marriage," a U.S. official said, "is better than a divorce."