The United States is suspending about one third of its annual aid to the Pakistani military
White House Chief of Staff Bill Daley told ABC television that Pakistan had "taken some steps that have given us reason to pause on some of the aid".
He said the US raid that killed Osama Bin Laden in May had affected ties but he insisted the relationship "must be made to work over time".
The $US800 million being withheld equates to about a third of the annual US security aid to Pakistan, US officials say.
Mr Daley said Pakistan had been an important ally in the fight on terrorism but until the two countries "get through these difficulties" the US will hold back some of the military aid.