"Most of these things that have happened in terms of global anti-terror, Pakistan has played a pivotal role... So it`s a little disquieting when we have comments like this," Foreign Secretary Salman Bashir said.
Bashir told the BBC that Pakistan had a "pivotal role" in fighting terrorism.
He said Panetta was entitled to his views but Pakistan had cooperated extensively with the US.
In his first interview with Time magazine since leading the operation that resulted in the killing of bin Laden near the Pakistani garrison city of Abbottabad, Panetta said US officials feared Pakistan could have undermined the mission by leaking word to its targets.
Bin Laden was shot dead during the raid by helicopter-borne US special forces early on Monday.
Bashir said the compound in Abbottabad, where bin Laden was found, had been identified as suspicious some time ago by Pakistan?s Inter-Services Intelligence agency.
It took the CIA`s greater resources to determine that it was the al-Qaeda leader`s hidout, he said.
Pakistan`s Foreign Office yesterday issued a statement that said the country`s civil and military leadership had no prior information of the US raid, which it described as an "unauthorised unilateral action" that should not be repeated.
The statement also defended the ISI, saying the spy agency had been sharing intelligence with the US about the "target compound" in Abbottabad since 2009.
However, several questions have been raised following the killing of bin Laden in a compound located just about 800 yards from the Pakistan Military Academy, one of the country`s main military training facilities.
US officials have questioned whether elements in Pakistan?s military and intelligence set-ups had known about bin Laden`s presence in the compound for as long as five years and were providing the world?s most wanted man a "support system".