The ministry said men were shot dead in a mountainous area in the western part of the province. Security forces watched men back to the area after the attack that killed seven Coptic Christian worshipers on their way to a monastery, the ministry said.
The ministry published photos of bodies claiming to be dead fighters and the weapons they held.
The team headed towards the Monastery of St. Samuel the Confessor, located south of Cairo in the western desert.
Six of the victims were from the same family, according to Ahram. A dozen people were also injured in the attack, he said.
ISIS has assumed responsibility for the Friday buses on Coptic Christians. In a statement published in the ISIS media agency, he said, "the ambush that targeted a Copos Christians bus on the way to St. Samuel's Monastery in Minya was carried out by Islamic state militants."
The statement was published by several ISIS channels in Telegram, a messaging application.
The team did not provide evidence to substantiate its allegations. CNN can not independently control the authenticity of the claim.
The US foreign ministry condemned the attack on a statement Friday.
"We express our condolences to the families of these innocent victims," Foreign Ministry spokesman Heather Naughter said. "We remain firm in support of Egypt's efforts to combat terrorism and violence against religious communities."
CNN's Eric Levenson contributed to this report.