North Korea lobbed a ballistic missile over Japan on Tuesday, South Korea's military said.

The missile was fired from the vicinity of Sunan in Pyongyang at around 5:57 a.m. and flew east, according to the Joint Chiefs of Staff (JCS), Yonhap News Agency reported.

"It passed through the sky over Japan," the JCS added.

Japan's broadcaster NHK also reported that the North's missile flew over the nation's territory.

Japan's Chief Cabinet Secretary Yoshihide Suga described it as an "unprecedented grave threat."

South Korea's presidential office Cheong Wa Dae immediately convened a National Security Council (NSC) session to discuss the issue.