The decision not to attend next week’s conference in the German city of Bonn came after a cabinet meeting chaired by Prime Minister Yousuf Raza Gilani.
Pakistan says the air strike violated its sovereignty and the mandate of international forces in Afghanistan.
Nato and the US government have apologised, calling the deaths tragic.
Pakistan responded to the air strike by cutting key Nato supply lines through its territory to Afghanistan.
Tuesday’s cabinet meeting came amid mounting public anger and growing demands from Pakistan’s opposition parties to sever all ties with the US.
“Pakistan has decided not to attend the Bonn conference as a protest,” a government official told Reuters after the cabinet talks in Lahore.
Pakistan’s military has denied reports that gunfire from its side of the border provoked the Nato strike on one of its checkposts.
Afghan officials have claimed that Nato forces were retaliating for gunfire from the Pakistani side of the volatile border on Saturday.
The incident has heaped further strain on already troubled relations between Nato and Pakistan, a crucial ally in the fight against the Taliban.