US officials have long been frustrated by what they see as Pakistan's reluctance to act against groups such as the Afghan Taliban and the Haqqani network that they believe exploit safe haven on Pakistani soil to launch attacks on neighbouring Afghanistan.
In August, Mr Trump outlined a new strategy for the war in Afghanistan, chastising Pakistan over its alleged support for Afghan militants.
He accused Pakistan of harbouring "agents of chaos" and providing safe havens to terrorist groups waging an insurgency against a US-backed government in Kabul.
The US official expressed hope that relations between the two countries could improve after a kidnapped US-Canadian couple and their three children were freed in Pakistan in October, after the couple was abducted in neighbouring Afghanistan.
"We have been very direct and very clear with the Pakistanis... we have not seen those changes implemented yet," General John Nicholson told reporters.
He added that he believed that senior Taliban leaders were based in Pakistan, while the lower level leadership was in Afghanistan.
Pakistan says it has done a great deal to help the United States in tracking down terrorists.
(Reporting by Idrees Ali and Phil Stewart; Editing by Alistair Bell)