U.S. says it is withholding about $ 800 million in military aid to Pakistan.
The White House chief of staff Bill Daley told ABC television that Pakistan had "taken steps that have given us reason to pause in the aid."
He said the U.S. attack who killedin May has affected the relationship, but he insisted the relationship "should be made to work on time."
The $ 800 million (£ 500 million) is equivalent to approximately one third of annual U.S. aid Pakistan on security, U.S. officials say.
In the figures presented to the IMF last fall, was Pakistan's defense expenditure in its budget in 2010-2011 put $ 6.41bn - an increase of $ 1.27 last year.
Speaking on the ABC program, This week, Mr. Daley has admitted that Pakistan was "an important ally in the fight against terrorism. They have had enormous amounts of terrorism."
He added: "It 'complicated relationship with a very difficult and complex the world It' clear that there is still a lot of pain, that the political system in Pakistan is heard in the track we did to get Osama Bin Laden, the President felt strongly about and we have no regrets over..
"Until we get through these difficulties, we maintain a bit of money that U.S. taxpayers have committed them."
The New York Times quoted U.S. officials before saying that the suspension of military aid amounted to about one third of annual aid to U.S. security in Pakistan.
The paper said the move was to show anger at the expulsion of U.S. military instructors and the U.S. pressure Pakistan to step up its fight against militants.
The Times said that some suspension of aid had been allocated as compensation for the redeployment of Pakistani troops on the border areas with Afghanistan to fight the militants. The other pieces were in military equipment.
Rajesh Mirchandani BBC's Washington says this is clearly a strengthening of the U.S. approach Pakistan - more carrot than the stick - but we fear that taking the money will stop the Pakistanis to cooperate on everything.
In a sign of the difficulty of Pakistan and the U.S. were last week, the top U.S. military officer Adm. Mike Mullen suggested that the Pakistani government "sanctioned" the killing of journalist Saleem Shahzad May
Mr. Shahzad was abducted near his home in Islamabad. His body was found two days later in the province of Punjab.
The Pakistani Minister of Information Firdous Ashiq Awan said Adm Mullen testimony was "extremely irresponsible and regrettable."
She said it would create difficulties in the relations between the sides and prove a setback in the war on terror.
The increase in U.S. drone attacks on militants in Pakistan along the border with Afghanistan is also a constant source of antagonism.