The report concluded both sides had made mistakes, blaming poor information and inadequate co-ordination between US and Pakistani forces on the ground.
The Pakistani military said the report was “short on facts”.
Pakistan closed its border with Afghanistan after the incident, cutting off vital Nato supply lines.
In a short statement, the Pakistani military said it did not agree with the findings of the report “as being reported in the media”.
“The inquiry report is short on facts,” it said.
The statement said the military would present a more detailed response “as and when the formal report is received”.
Islamabad, a vital partner in the fight against militants in the region, has demanded a formal US apology.
In its report, the US military admitted it bore significant responsibility for the deaths in Mohmand tribal agency on 26 November, and expressed “deep regret” for the “tragic loss of life”.
Pakistan responded furiously to the killings of its soldiers.
As well as shutting its border with Afghanistan, which Nato relies on heavily for deliveries of fuel, ammunition and other supplies, it also refused to attend the Bonn conference on Afghanistan earlier this month