WASHINGTON -- The CIA is downplaying tensions in U.S.-Pakistani relations after Pakistan's military spy agency arrested five informants for the CIA whose work over several months helped lead to the U.S. raid that killed Usama bin Laden.

Among those arrested was a Pakistani Army major serving as a doctor and the owner of the safe house used by the CIA to spy on bin Laden at his Abbottabad, Pakistan, compound.

The major, who is said to have copied license plate numbers of vehicles entering the compound, was arrested, sources told Fox News on Wednesday, because the safe house was not known to Pakistan's Inter-Services Intelligence Agency.

However, the ISI is denying the arrest, saying the story is "false and baseless."

The conflict is just the latest in a series of reports of trouble in ties. Over recent weeks, U.S. officials have repeatedly tipped off Pakistanis to bomb-making and weapons facilities only to learn that Pakistani military showed up to find empty sites.

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Officials said the arrests of the informants was just the latest evidence of the fractured relationship between the two nations since the raid by Navy SEALs to take out bin Laden.

The CIA, however, said CIA Director Leon Panetta is working closely with the Pakistanis to strengthen relations.

"We have a strong relationship with our Pakistani counterparts and work through issues when they arise," CIA spokeswoman Marie Harf told Fox News."Director Panetta had productive meetings last week in Islamabad. It's a crucial partnership, and we will continue to work together in the fight against Al Qaeda and other terrorist groups who threaten our country and theirs."

Senate Republican leader Mitch McConnell told Fox News that the arrests shows that the U.S.-Pakistani relations is a "mixed bag."

"You know there are parts of the Pakistani intelligence service and the government and the military that are sort of on our side and parts of it that aren't," he said. "I think all of us know there must've been a faction inside the Pakistani government that was aware of Usama bin Laden's presence for five years. So Pakistan is a very mixed bag. There are people there who are allied with us and people there who aren't."

State Department spokesman Mark Toner wouldn't address the arrests on Wednesday. He simply acknowledged the essential yet challenging relationship.

"I think we've been up front about challenges in the relationship, but we've also been consistent in saying that Pakistan and the U.S. need each other," he said. "We need to work through these challenges because it's in both our long-term -- short-term, frankly -- interests to do so."

One State Department official, speaking on condition of anonymity, expressed frustration with the Pakistani authorities.

"Why arrest those who helped in finding Usama bin Laden when Pakistan should be hunting down militants as it keeps promising to do but never delivering anything of substance?" the official asked.

The New York Times, which was first to report the arrests, said that during a closed briefing last week, members of the Senate Intelligence Committee asked Deputy CIA Director Michael Morell  to rate Pakistan's cooperation with the United States on counterterrorism operations, on a scale of 1 to 10.

"Three," Morell reportedly answered.

White House spokesman Jay Carney said Wednesday he wasn't going to give a scaled assessment on the ties with Pakistan, nor would he comment on the reports of arrests.

"I am simply saying we are actively engaged with the Pakistanis. It's a complicated relationship that is not perfect and requires attention. ... It's important to our national security interests. ... They have been reliable in providing important information in successful operations against terrorists," he said.

Outgoing Defense Secretary Robert Gates downplayed the arrests during questioning at a Senate Appropriations Defense subcommittee hearing.

"Well, first of all, based on 27 years in the CIA and four and a half in this job, most governments lie to each other," he said. "It's the way business gets done."

When asked by Sen. Patrick Leahy, D-Vt., if they also arrest the people that help when they say they're allies, Gates said, "Sometimes.And sometimes they send people to spy on us. That's the real world that we deal with."

Fox News' Jennifer Griffin and Dominic Di-Natale contributed to this report.