North Korea fired multiple ballistic missiles on Thursday, including one that triggered an alert for residents in parts of central and northern Japan to seek shelter, the latest in a record year of missile testing by the nuclear-armed North.

Despite an initial government warning that a missile had overflown Japan, Tokyo later said that was incorrect.

The launches came a day after North Korea fired at least 23 missiles, the most in a single day, including one that landed off South Korea's coast for the first time.

Residents of Miyagi, Yamagata and Niigata prefectures in northern Japan were warned on Thursday to seek shelter indoors, according to the J-Alert Emergency Broadcasting System.

Japanese Defence Minister Yasukazu Hamada said the government had lost track of the first missile over the Sea of Japan, prompting it to correct its earlier announcement that it had flown over Japan.

"We detected a launch that showed the potential to fly over Japan and therefore triggered the J Alert, but after checking the flight we confirmed that it had not passed over Japan," Hamada told reporters.

The first missile flew to an altitude of about 2,000 kilometres and a range of 750 kilometres, he said. Such a flight pattern is called a "lofted trajectory", in which a missile is fired high into space to avoid flying over neighbouring countries.

In brief comments to reporters a few minutes later, Prime Minister Fumio Kishida said, "North Korea's repeated missile launches are an outrage and absolutely cannot be forgiven."

About half an hour after the launch was first reported, Japan's Coast Guard said the missile had fallen.

The Yonhap news agency reported the first missile went through stage separation, suggesting it may be a long-range weapon such as an intercontinental ballistic missile (ICBM).

South Korea's Joint Chiefs of Staff said the long-range missile was launched from near the North Korean capital of Pyongyang.

About an hour after the first launch, South Korea's military and the Japanese coast guard reported a second and third launch from North Korea. South Korea said both of those were short-range missiles fired from Kaechon, north of Pyongyang.

After North Korea's launches on Wednesday, including one missile that landed less than 60 km (40 miles) off South Korea's coast, South Korean President Yoon Suk-yeol described the flights as "territorial encroachment" and Washington denounced them as "reckless".

South Korea issued rare air raid warnings and launched its own missiles in response after Wednesday's barrage.

The launches came after Pyongyang demanded the United States and South Korea stop large-scale military exercises, saying such "military rashness and provocation can be no longer tolerated".

The allies have been conducting one of the largest air exercises ever, with hundreds of South Korean and US warplanes, including F-35 fighters, staging around-the-clock simulated missions.

On Oct 4, North Korea launched a ballistic missile over Japan for the first time in five years, prompted a warning for residents there to take cover. It was the farthest North Korea had ever fired a missile.