"Following frequent attacks on communities around the Plateau-Taraba border by some militiamen, we carried out an operation to flush out members of these murderous gangs," Captain Ikedichi Iweha of the special task force told AFP.
He said the soldiers engaged the gunmen in a fierce battle, leaving several people dead.
"I don't have any information on the exact death toll. But several people were killed during the gun duel," he said.
Iweha denied civilians were killed after local media said at least 30 people died when soldiers stormed into Kadarko, Kurmi and Wadata areas on Friday and yesterday in 40 trucks, burning houses and shooting indiscriminately.
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Media reports said the soldiers stormed the communities to avenge the death of four soldiers by some militiamen near the border with neighbouring Taraba state.
Plateau state falls in Nigeria's so-called "Middle Belt", where the mainly Christian south meets the majority Muslim north.
The region has seen a wave of sectarian and communal violence in recent years, claiming hundreds of lives.