The collapse is believed to have happened on October 10, but South Korea's Yonhap news agency, said it was still unclear when the disaster happened.
The network claimed the tunnel collapse the ground around the site was weakened by North Korea's sixth nuclear test, which was carried out at the same site.
It comes a day after Seoul warned that one more North Korean nuclear detonation could destroy its mountain test site and trigger a radiation leak.
South Korea says any future nuclear test by Kim Jong-Un risks collapsing the location set aside for launching missiles.
Seoul detected several earthquakes near the hermit nation's nuclear test site in the country's northeast after its sixth and most powerful bomb explosion in September.
Experts say the quakes suggest the area is now too unstable to conduct more tests there.
South Korea's weather agency chief Nam Jae-Cheol made the comments Monday during a parliament committee meeting.
Last month US experts issued a similar warning, stating a second nuclear test site in North Korea's northwest could cave in but that it won't be abandoned.
Five of Pyongyang's recent tests have been carried out under Mt Mantap at the Punggye-ri military base, in North Korea's northwest.
But now the base is said to be suffering from "Tired Mountain Syndrome" after three small earthquakes after the blasts.