Islamabad has expressed disappointment at certain remarks made recently during deliberations in the US Senate about the presence of terrorists in Pakistan.

Some lawmakers and Commander of US forces in Afghanistan General John Nicholson said at last week's Congressional hearing that the Afghan Taliban and the Haqqani Network still have safe haven in Pakistan.

Nicholson had also pushed the Donald Trump administration to conduct a "holistic review" of relationship with Pakistan.

Pakistan's Foreign Ministry on Monday said it was upset at the allegations of terrorist centres on Pakistani soil.

"We are disappointed with some of the assertions and insinuations made in recent discussions about terrorist safe havens in Pakistan that we feel are not in sync with the current situation on the ground," Foreign Ministry spokesman Nafees Zakaria said in response to the discussions in the US on Afghanistan and Pakistan-US relations.

Zakaria, in a statement, said the discussions spoke of multiplicity of factors and singling out Pakistan and pinning the entire blame on the country for the situation in Afghanistan was "neither fair nor accurate".

He said Pakistan has been successful in eliminating the command and control structure of terrorist outfits operating across the Pakistan-Afghan border.

"Terrorist groups attacking Pakistan have safe havens in Afghanistan. The recent elimination of terrorists in Afghanistan involved in a number of heinous acts of terror in Pakistan clearly demonstrates the existence of safe havens in Afghanistan for elements attacking Pakistan," he said.

The spokesman said the nexus between Islamic State militant group and Tehreek-e-Taliban Pakistan is a source of deep concern for Islamabad.

"We need to prevent the emergence of new and more virulent entities committed to spreading chaos and insecurity in the region. This calls for closer cooperation based on confidence and trust. Pointing fingers and throwing blame at others would be unhelpful and counter-productive," he said.