Seoul's unification ministry conducted check-ups on 30 North Koreans who left before January 2016.
It shook the country early Saturday morning.
The South and North Development (SAND) research institute reported the situation in a village near the Punggye-ri nuclear facility.
The Punngye-ri underground facility hosted the country's sixth and most powerful nuclear test to date.
The nuclear test has made the mountainous location unsuitable as a base.
Pyongyang wants the U.S. to halt its military exercises with South Korea in return.
Some experts say the likelihood of another test has increased after a failed missile launch on Friday.
South Korea said the exercises would be the largest ever following the North's nuclear and rocket tests.
South Korea's Intelligence Agency briefed ruling party parliamentarian