Munter was apparently "frustrated" that the CIA and Pentagon were not on the same page as the US State Department as far as policy on Pakistan is concerned, The News daily quoted its sources as saying.
With the recent coordinated attacks across various places in Afghanistan, including the heavily guarded diplomatic zone in Kabul, the US may be far from exploring the option of the Haqannis playing mediator.
The Obama administration will not swerve from plans to move into an advisory role in Afghanistan, US officials said on Monday, despite the killing of US advisors over the weekend.
The report alleges that the Pakistan secret service is behind the rise of the Taliban and are helping its fight against US and NATO forces.
Pakistan expects to reopen supply routes to NATO forces in Afghanistan, but will impose tariffs, a senior security official told Reuters on Thursday.
Public sentiment runs high in Pakistan against the US; credibility of army under suspicion.
Pakistan has cut supplies to the NATO along the Afghanistan border, and lodged a strong protest over the attack along the border that reportedly killed 28 Pakistani soldiers.