The object had not been identified and its radar course was being investigated, the military said in a statement.
One official told AFP it appeared to be a drone.
The official gave no details, but previous drones flown across the border have been similar in size to hobby drones.
The military did not indicate whether the object had been shot down, or had gone back over the border, one of the most heavily-fortified locations in the world.
The South's Yonhap news agency said around 90 rounds were fired from a machine-gun at the object.
Tensions are high in the region over the nuclear-armed North's weapons ambitions, and the incident comes only two days after its latest missile launch.
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