"At around 7:10 am (1010 GMT), two projectiles were launched from the eastern coast of North Korea," Yoshihide Suga told reporters.
"One of them appears to have fallen into waters... inside Japan's exclusive economic zone," the chief cabinet secretary said.
The comments came after South Korea's military said the North on Wednesday fired projectiles toward the sea, a day after Pyongyang signalled a resumption of nuclear talks with the US.
Japanese Prime Minister Shinzo Abe had instructed his ministers to investigate, Suga said. (AFP)