It said Armenian units opened small arms fire on Azerbaijani soldiers in Sadarak in the north of Nakhchivan, an exclave of Azerbaijan that borders Armenia, Turkey and Iran.
The ministry's statement did not say if there had been any casualties.
Reuters could not independently verify the reported incident. It came against the background of rising tensions between Armenia and Azerbaijan in recent days.
(Reporting by Nailia Bagirova, writing by Mark Trevelyan, editing by Mark Heinrich)
