US officials have said there was no evidence indicating leaders in Islamabad knew Osama Bin Laden had been hiding in Pakistan.
But defence secretary Robert Gates said he believed "somebody" in Pakistan knew the whereabouts of the al-Qaeda chief.
Top military officer Adm Mike Mullen said it might take a while to find out if Bin Laden had Pakistani protectors.
Amid increasing pressure from US lawmakers, both men advised against cutting off aid to Pakistan.
In a joint news conference at the Pentagon, Mr Gates and chairman of the Joint Chiefs of Staff Adm Mullen said the US must continue to work with Pakistan and provide aid to the country.
But the officials said Pakistan must take action to eliminate the safe havens where militants are allegedly hiding along the border with Afghanistan.
Mr Gates said that though he believed "somebody knew" Bin Laden was hiding in the country, he had seen "no evidence at all" that the senior leadership knew before the raid.
"In fact, I've seen some evidence to the contrary," he said.
The Pentagon has come under increasing pressure from US lawmakers to find out if Pakistan knew of Bin Laden's whereabouts.
US intelligence agencies have been analysing notebooks, computer data and other materials taken from Bin Laden's compound in Abbottabad since it was raided by American forces early on 2 May (1 May US time).
Mr Mullen said the Pakistani military's image had been tarnished by the US operation, which took place without the knowledge of the Pakistani government.
On Saturday, Pakistan's parliament condemned the raid and called for an end to unilateral action within its borders, including attacks on suspected militants by US drones.