The report said Seoul's military did not provide further details and was analyzing the launch.
Pyongyang fired a total of ten short-range ballistic missiles toward the Sea of Japan on Thursday, Yonhap cited the South's military as saying.
Japanese broadcaster NHK reported, citing the Japan Coast Guard, that a projectile, "which could have been a ballistic missile, has already landed."
The report also cited a spokesperson for the Japanese Defense Ministry as saying that the suspected ballistic missile has landed outside Japan's exclusive economic zone.
Japanese Prime Minister Fumio Kishida has strongly condemned the North's launch and expressed hope for cooperation with the United States and South Korea.
Japanese news agency Kyodo reported, citing the South's military, that the missiles traveled about 350 kilometers (217 miles) before landing at sea.