"Two militants were killed in a skirmish," Igor Kovalenko said by telephone. "The site is being examined and the nearby area is currently being combed."
A Russian prosecutor said earlier that troops were engaged in a shootout with gunmen subordinate to Al-Qaeda leaders on the Ingush-Chechen border.
"We have received reports saying the militants are under the direct command of Al-Qaeda leaders," a source in Russia's Prosecutor General's Office said.
He said one gunman had been killed and was being identified.
"The others have been blocked and special units are continuing to fight with them. The militant group's strength is being identified at the moment," he said.
Federal losses were not reported.
"The group was uncovered during an investigation into militant groups' activities in the North Caucasus," he said. "A suspect arrested the other day spoke of the group active in Ingushetia," he said.