The US' admiral Mike Mullen had accused Pakistan's spy agency of backing the Haqqani group in a recent attack in Kabul where 25 people were killed in an assault on the US embassy and other buildings.
But the Pakistani government has vehemently denied such claims.
Cooperation between the two countries has deteriorated since the raid in May where US forces killed Osama bin Laden without telling Islamabad they were going in.
Al Jazeera's Rosiland Jordan reports from Washington.
