It follows claims by Afghan officials that Nato forces were retaliating for gunfire from the Pakistani side of the volatile border region on Saturday.
On Sunday Pakistan’s army chief led mourners as those killed in the strike were buried at military headquarters.
Nato has apologised, calling it a “tragic unintended incident”.
But the attack has heightened already tense relations between Pakistan, the US and Nato.
Pakistan reacted angrily to the attack, which took place at two remote border posts in Pakistan’s tribal district of Mohmand in the early hours of Saturday morning. Several protests against Nato’s actions have been held across the country.
Pakistan’s Prime Minister Yousuf Raza Gilani called it a “grave infringement of Pakistan’s sovereignty” and officials responded by cutting key supply Pakistani lines to Nato in Afghanistan.
But unnamed Afghan officials quoted in The Wall Street Journal said that Saturday’s attack was called in to shield Nato and Afghan forces who were under fire while targeting Taliban fighters. One official quoted in the paper says that Kabul believes the fire came from an army base.
“This is not true. They are making up excuses. What are their losses, casualties?” Pakistani army spokesman Maj-Gen Athar Abbas said in a text message in response to the allegations.
Maj Gen Abbas has also said that the raid went on for more than an hour and continued even after local commanders contacted Nato telling them to stop the strike, according to the Associated Press news agency.
Nato chief Anders Fogh Rasmussen said he had written to Mr Gilani to “make it clear that the deaths of Pakistani personnel are as unacceptable and deplorable as the deaths of Afghan and international personnel”.
Nato has said it is investigating what happened.
In a joint statement, US Secretary of Defense Leon Panetta and Secretary of State Hillary Clinton, offered their condolences for the loss of life, backed the investigation into the incident and stressed the “importance of the US-Pakistani partnership, which serves the mutual interests of our people”.