Kandahar's governor, Assadullah Khalid, says Commander Abdul Razzak has been temporarily replaced at his post while an investigation into the killings proceeds.
Razzak claims the Pakistanis were Taliban fighters and had attacked border police after crossing illegally into Afghanistan from Pakistan.
But Saqib Aziz, a Pakistani official in the border town of Chaman, says the Pakistanis were from the Nurzai tribe and were killed because of a blood feud with Razzak's clan.
Pakistan says the victims were trying to travel to a festival in northern Afghanistan marking the spring festival Norouz.