The Pakistani intelligence agency, the ISI, admits to being extremely embarrassed it was unaware that Osama bin Laden was living in a compound close to a military academy.
An ISI official says Pakistani forces raided the compound in 2003 in pursuit of another Al Qaeda operative but it had been "off their radar" since then.
The killing of the Al Qaeda leader was announced late on Sunday night in Washington by President Barack Obama.
The government of Pakistan has categorically denied any knowledge of the raid before it took place on Sunday.
President Asif Ali Zardari has also denied suggestions that his government may have sheltered Osama bin Laden.
He has published an opinion piece in the Washington Post newspaper, defending his nation's work in the global war on terrorism.
Mr Zardari said Pakistan had ''never been and never will be the hotbed of fanaticism that is often described by the media'''.
''Such baseless speculation may make exciting cable news, but it doesn't reflect fact,'' he said.
''Pakistan had as much reason to despise al-Qaeda as any nation. The war on terrorism is as much Pakistan's war as it is America's.''
White House comment
White House counter-terrorism adviser John Brennan said there had been concern that Pakistani forces would deploy to counter the US Navy Seal team conducting the raid but it had avoided any confrontation.
Mr Brennan had said it was "inconceivable that Bin Laden did not have a support system" in Pakistan.
He estimated Bin Laden had been living in the compound in Abbottabad for five or six years.
The BBC reports the compound is a few hundred metres from the Pakistan Military Academy - the equivalent of West Point or Sandhurst.