CIA, ISI locked in aggressive spy battles

But the CIA had its doubts. Before long, the suspicious officers had concluded that Pakistan's spy agency, the Inter-Services Intelligence, was trying to run a double agent against them.

CIA officers alerted their Pakistani counterparts. Pakistan promised to look into the matter and, with neither side acknowledging the man was a double agent, the affair came to a polite, quiet end.

The incident, recounted by former US officials, underscores the schizophrenic relationship with one of America's most crucial counter terrorism allies.

Publicly, officials credit Pakistani collaboration with helping kill and capture numerous al-Qaida and Taliban leaders. Privately, that relationship is often marked by mistrust as the two countries wage an aggressive spy battle against each other.

The CIA has repeatedly tried to penetrate the ISI and learn more about Pakistan's nuclear programme; and the ISI has mounted its own operations to gather intelligence on the CIA's counterterrorism activities in the tribal lands and figure out what the CIA knows about the nuclear programme.

Bumping up against the ISI is a way of life for the CIA in Pakistan, the agency's command center for recruiting spies in the country's lawless tribal regions.
Officers there also coordinate Predator drone airstrikes, the CIA's most successful and lethal counterterrorism program. The armed, unmanned planes take off from a base inside Pakistani Baluchistan known as "Rhine."

"Pakistan would be exceptionally uncomfortable and even hostile to American efforts to muck about in their home turf," said Graham Fuller, an expert on Islamic fundamentalism who spent 25 years with the CIA, including a stint as Kabul station chief.

That means incidents such as the one involving nuclear fuel rods must be resolved delicately and privately.

"It's a crucial relationship," CIA spokesman George Little said. "We work closely with our Pakistani partners in fighting the common threat of terrorism. They've been vital to the victories achieved against al-Qaida and its violent allies. And they've lost many people in the battle against extremism. No one should forget that."

Details about the CIA's relationship with Pakistan were recounted by nearly a dozen former and current US and Pakistani intelligence officials, all of whom spoke on condition of anonymity because they were not authorised to discuss the matter.

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