A news report yesterday quoting US sources said that the hospital was hit as it was believed to be used by a Pakistani operative aiding Taliban militants.
Foreign Office spokesman Qazi Khalilullah rejected the allegations levelled in the news report. "Allegations implicating Pakistan are baseless," he said.
"I want to reiterate that non-interference in Afghanistan's internal affairs is a key pillar of our Afghan policy," he said.
The attack on October 3 killed at least 22 patients and hospital staff for which the Doctors Without Borders (MSF) charity blamed the US military, forcing President Barack Obama to issue an apology.
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A Pakistani security official said on condition of anonymity that blaming a "Pakistani operative" was an afterthought as pressure was mounting on the US to come clean on the attack.
"If they had reports about presence of any suspect, then ground troops could have been involved than bombing the entire facility," he said.
Obama has now said that US troops will stay on in Afghanistan till the end of 2017.