"This is frivolous, to put it mildly. We are committed to non-interference in Afghanistan and expect all other states to strictly adhere to this principle," Foreign Office spokesman Abdul Basit said.
"We are committed to an Afghan-led and Afghan-owned reconciliation process... A stable and peaceful Afghanistan is in our own interest and we are very much cognizant of this," Basit said in a text message sent to PTI.
Pakistan, he said, had "suffered enormously because of the long conflict in Afghanistan".
Earlier in the day, BBC quoted a secret NATO report as saying that the Taliban in Afghanistan were being "directly assisted by Pakistani security services".
The report, based on 27,000 interrogations with over 4,000 captured militants, claimed the Taliban remained defiant and have wide support among the Afghan people.
The report was leaked just as Foreign Minister Khar arrived in Kabul for talks aimed at reviving Pakistan- Afghanistan cooperation for the reconciliation process in the war torn country ahead of the withdrawal of US troops.
Talks between the two sides had broken down last year after Afghan officials blamed elements within Pakistan for the assassination of Afghan High Peace Council chief Burhanuddin Rabbani.
The NATO report alleged that Pakistan knew the locations of senior Afghan Taliban leaders.
BBC said the report on the state of the Taliban "fully exposes for the first time" the relationship between Pakistan's Inter-Services Intelligence agency and the Taliban.
"Pakistan's manipulation of the Taliban senior leadership continues unabatedly," the report was quoted as saying by BBC.
In Washington, Pentagon spokesman Capt John Kirby said: "We have long been concerned about ties between elements of the ISI and some extremist networks."
The BBC had angered Pakistan's security establishment last year when it broadcast a two-part documentary "Secret Pakistan" that accused elements of the ISI of complicity with Taliban militants.
Pakistan had also reacted angrily to a cross-border NATO air strike that killed 24 of its soldiers in November last year and Prime Minister Yousuf Raza Gilani has sought a parliamentary review of relations with the US.