Experts say that although the harm the episode has done to the relationship is not irreparable, it will breed mistrust between the two sides at a time when Washington is urging Islamabad to shoulder a bigger responsibility in the war on terrorism, the Los Angeles Times reports.
US officials suspect Pakistan's intelligence community, which has long been plagued by divided allegiances, of disclosing the identity of the CIA station chief in Islamabad, who was sent out of the country following the revelation.
Meanwhile, Pakistan's main spy agency, the Directorate for Inter-Services Intelligence (ISI), has denied any role in the breach.
A Pakistani intelligence source said that the agency did not know the source of the disclosure. "That's a mystery we have not been able to solve," the source added.
US suspicions immediately fell on the ISI, and a possible motive may have been retaliation for a lawsuit filed in New York last month that named the ISI's chief, Lt. Gen. Ahmed Shuja Pasha, as a defendant, and accused his agency of supporting the militants who carried out the 2008 Mumbai terror attacks that killed about 170 people.
Experts said that some ISI operatives were sympathetic to the cause of Afghan Taliban militants battling US and NATO forces in Afghanistan, and could have been willing to "out" the CIA station chief.
"There may be elements within the Pakistani intelligence community who still have sympathies for [militants] in the tribal areas, especially Pashtun officers," said Javed Hussain, a retired Pakistani special forces commander and now a security analyst.
Some of those officers have ties with Taliban militants that date to the Soviet occupation of Afghanistan, said Hussain, adding, "It's hard to tell these officers, 'OK, switch off.'"
Talat Masood, a retired Pakistani general, said that what made the disclosure of the agent's identity especially problematic was that it was the latest in a series of events that have ratcheted up tensions between Washington and Islamabad.
The US has been working to mend ties with Pakistan following a cross-border air strike on September 30 that had mistakenly killed three Pakistani soldiers near the border with Afghanistan, in retaliation to which Pakistan had shut down its border crossing used by Afghan-based NATO convoys for some days.
"There is continuous tension that builds up because of these incidents, and that's not good," Masood said. "We want relations based on mutual confidence, and this is lacking. There are too many small incidents that are creating, if not a rupture in relations, certainly significant problems. And this can only be of benefit to the militants."