Japan's top government spokesperson says a system glitch is to blame for the issuance of a false missile alert in some parts of the country following North Korea's missile launch on Tuesday.

The alert was sent out in nine municipalities on Tokyo's Pacific islands through the nationwide J-ALERT emergency warning system, although there was no need for alarm in the areas.

Chief Cabinet Secretary Matsuno Hirokazu said on Wednesday that an investigation found a flaw in the system.

Matsuno apologized to residents of the nine municipalities for causing concern. He added the government will swiftly improve the system and work to prevent any similar incidents.