Afghan officials initially said the troops attacked suspected militants near the town of Spin Boldak in Kandahar Province after receiving intelligence reports that insurgents were preparing to enter Afghanistan.
However, Pakistan says those killed were Pakistani tribesmen traveling to a festival, and not members of the Taliban, the radical movement deposed from power by the U.S.-led invasion in 2001.
Pakistan's Foreign Ministry lodged a formal complaint with Afghanistan on March 23.
The bodies of the men have been returned to Pakistan for burial.
(AFP, AP, Reuters, dpa)