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Relations between U.S. and Pakistani intelligence agencies have hit a rough patch. That's after revelations that an American in Pakistan, who's been jailed for shooting two men, was secretly working for the CIA.

As NPR's Julie McCarthy reports from Islamabad, the disclosure has also deepened public skepticism about what the U.S. is doing in Pakistan.

JULIE McCARTHY: Not until nearly one month into the ordeal that has tested U.S.-Pakistan relations did the Americans reveal what Raymond Davis does. A U.S. official familiar with the investigation confirmed that Davis works for the CIA, as a contractor providing security to American officials in the region.

The CIA team Davis was affiliated with in Lahore reportedly tracked down Pakistani militant groups. But U.S. officials deny that Davis himself was involved in militant surveillance or spying.

A senior official with Pakistan's intelligence agency, the ISI, wondered quote, how many other Raymond Davises were running around. The same official said the incident which blew Davis' cover, and killed three Pakistanis, has virtually thrown into question CIA-ISI relations, which had been improving. He said the onus of not stalling the relationship now rests squarely on the CIA.

Analyst and author Ayesha Saddiqa says from the Pakistani agency's point of view, the rules were flouted, and the Americans appeared to have set up a parallel structure in Pakistan.

Dr. AYESAH SADDIQA (Political Analyst): So there is a fair amount of cooperation going on in fighting the war on terror. But what the ISI suspected, and it probably saw, was that there were these operatives who went beyond the regular channels of cooperation between the two countries, and were doing something of their own.

McCARTHY: A document provided to NPR show that Davis is assigned to the U.S. embassy staff, a position that typically affords diplomatic immunity. But the revelation that Davis is also CIA confirms the deepest suspicions of many Pakistanis, who questioned what a diplomat was doing in a dodgy area of Lahore when he fatally shot two men after he said they threatened him with a gun.

Mr. MOSHARRAF ZAIDI (Political Columnist): There's nothing at all that's illegitimate about the angst and the anguish and the fear in Pakistan.

McCARTHY: Columnist Mosharraf Zaidi says Davis represents the thin edge of a so-called covert war - a war that includes, for example, the CIA drone missile program. He says both countries believe the war is merited to beat back a threat to their national security. But Zaidi says for all the problems it may be solving, it's also creating significant new ones.

Mr. ZAIDI: There's a covert war going on, and neither country is in a position to embrace that and to be transparent about that. And if you can't be transparent about something and people are dying, in the obfuscation and in the lack of that transparency, you have a real, serious public policy problem. You have that problem in the U.S., and you have it in Pakistan.

McCARTHY: Ayesha Saddiqa says the case of Raymond Davis, and the way it has incited anti-Americanism...

Dr. SADDIQA: I've never seen it this way - never.

McCARTHY: ...has presented Pakistan the chance to recalibrate its strategic calculation, which until now had been configured against India.

Dr. SADDIQA: What is now added on to that is anti-Americanism, anti-Westernism, confidence that the nuclear weapons give Pakistan the right to A, expand its influence in the region and B, to look the U.S. in its eyes and say, I'll compete with you, I'll contest you - that the U.S. must treat Pakistan equally.

McCARTHY: Saddiqa says the worst-case scenario for Davis is that he is tried in Pakistan, convicted on murder charges, and sentenced to death. But despite the soured relations between the powerful intelligence communities of both countries, Saddiqa says she expects a compromise.

Dr. SADDIQA: I think they want to settle somewhere in the middle. The timing, and what will it cost the U.S., that's the unknown.

McCARTHY: Julie McCarthy, NPR News, Islamabad.

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