Ministry spokesman Yousuf Stanekzai said an assessment team had been sent to the site of the grave in the eastern province of Paktika - discovered last month after shoes, jackets and uniforms rose to the surface.
Stanekzai said on Thursday that the grave is believed to contain the bodies of Afghan soldiers of the communist government of former President Najibullah who were killed after surrendering to mujahedeen fighters.
Another Interior Ministry official who spoke on condition of anonymity as he was not authorised to speak to media, said the grave contains more than 500 bodies. He did not know who had found the grave and alerted authorities.
Najibullah's regime ruled Afghanistan after the Soviet occupation ended in 1989 until April 1992.
Kabir Ranjbar, a historian and an associate of the late president, said there were several massacres of communist soldiers in the south and east of the country in the months before the collapse of Najibullah's government.
Hundreds of thousands of Afghans died during the Soviet occupation and the bitter civil war that followed.
Dostum's militia is said to have
suffocated hundreds of prisoners
Officials have also reported mass graves in northern Afghanistan from fierce fighting during the war that ousted the Taliban in late 2001.
Human rights groups have called for an investigation into reports that hundreds of Taliban prisoners held by the militia of ethnic Uzbek strongman Abdul Rashid Dostum, suffocated in metal shipping containers.
Several mass graves were discovered in a northern desert.