ISLAMABAD – Pakistan’s main spy agency denied it had unmasked the CIA’s station chief in Islamabad, and warned such allegations could damage its already fragile counterterrorism alliance with the United States.

The CIA pulled its top spy out of Pakistan on Thursday amid death threats after his name emerged publicly a few weeks ago from a Pakistani man threatening to sue the CIA over the alleged deaths of his son and brother in a 2009 U.S. missile strike. The attorney involved with the complaint said he learned the name from Pakistani journalists.

But the station chief’s outing has spurred questions about whether Pakistan’s spy service might have leaked the information. Lawsuits filed last month in New York City in connection with the 2008 terror attacks in Mumbai, India, also may have raised tensions by naming Pakistan’s intelligence chief as a defendant.

The recall of the top American intelligence official in Pakistan comes at a delicate time.

The White House over the past week released the results of a review of progress in the war in neighboring Afghanistan. The report included the conclusion that the existence of safe havens for militants on Pakistan’s side of the border remained a major obstacle to defeating the Taliban and al-Qaida.

Pakistan’s assistance in clearing those militant hideouts — and providing intelligence to help the U.S. pinpoint targets for its covert, drone-fired missile strikes — is considered crucial. A breakdown in the relationship with Pakistani intelligence could be a major blow to the U.S.

An official with Pakistan’s Inter-Services Intelligence agency, its lead spy agency and a powerful force in the country, said Saturday any suggestions it outed the station chief were “a slur.”

In particular, he denied the notion that the U.S. lawsuits had spurred the ISI to retaliate.

The plaintiffs in the U.S. lawsuits include relatives of victims in the Mumbai attacks, which left 175 people dead. The suits repeat allegations that the ISI “has long nurtured and used international terrorist groups.”

Pakistan has denied any government involvement in the attacks in India, and has detained seven suspects in the case.