The CIA ruled out Pakistan as a partner in the Navy Seals’ operation to capture or kill Osama bin Laden because it feared Islamabad may alert the Al-Qaida leader, according to CIA Director Leon E Panetta.

In an interview with Time magazine, Panetta said: “It was decided that any effort to work with the Pakistanis could jeopardise the mission. They might alert the targets.” Panetta briefed US lawmakers on the raid on Tuesday.

He said Washington is trying to get to the bottom of the Pakistan’s “troubling” role in its professed ignorance about Laden’s whereabouts and whether it was involved or incompetent. “Either they were involved or incompetent. Neither place is a good place to be,” Panetta said.

Meanwhile, Pakistan’s Foreign Ministry in a lengthy statement expressed “deep concerns and reservations” over the US operation, which, it claimed, was “without prior information or authorisation from Islamabad.”

“This event of unauthorised unilateral action cannot be taken as a rule,” it said. Pakistan, a key ally in the US war in Afghanistan, received $1.3 billion in US aid last year.

White House spokesman Jay Carney on Tuesday described the US-Pakistan relationship as “complicated but important.”

Unidentified officials in the ISI were quoted in some reports as saying the agency was unaware that Laden was hiding in a million-dollar mansion in Abbottabad, 30 miles from the Pakistani capital, Islamabad. The compound was less than a mile from the elite Pakistan Military Academy in Kakul.

Some Pakistani officials said Laden had been living in the house for the past few months. The comments conflicted with those from other Pakistani officials who said they were unaware that the terrorist leader was in Abbottabad.

US President Barack Obama’s counterterrorism adviser, John Brennan, told CBS’ “Early Show” that Laden had been living in the mansion for the past five or six years.

Abbottabad and its surrounding areas had been under “sharp focus of intelligence agencies since 2003 resulting in a highly technical operation by the ISI which led to the arrest of high value Al-Qaida target in 2004,” according to a statement by the Pakistan Government. The ISI had been sharing information regarding the Abbottabad house with the CIA and “other friendly intelligence agencies” since 2009 and the intelligence flow indicating the presence of “foreigners” in the outskirts of Abbottabad continued until mid-April, it added.

The statement said the CIA had taken advantage of “much superior technological assets” and “exploited the intelligence leads given by us to identify and reach Laden.” It said the US helicopters had entered Pakistani airspace by using blind spots in radar coverage caused by the hilly terrain. According to some Pakistani media reports, the US helicopters took off from Ghazi airbase in Pakistan.