South Korean military said North Korea fired a "long-range ballistic missile", its third this week, on Thursday, as South Korean President Yoon Suk Yeol headed to Tokyo to boost ties in the face of Pyongyang's growing aggression.

"Our military detected one long-range ballistic missile fired from around the Sunan area in Pyongyang," Seoul's Joint Chiefs of Staff said, adding that it was an ICBM-class missile.

Japan's defence ministry also confirmed the launch, tweeting that the missile was expected to fall "outside Japan's exclusive economic zone, about 550 km (341 miles) east of the Korean Peninsula."

Japan's coast guard also issued a warning to vessels to be vigilant about fallen objects.

The launch is Pyongyang's third show of force since Sunday and comes as South Korea and the United States stage their largest joint military drills in five years.

The Thursday launch also came hours before the leaders of South Korea and Japan were due to meet in Tokyo, with Pyongyang's missile and nuclear programmes high on the agenda.

That summit – the first in 12 years – comes as the two neighbours seek to mend diplomatic ties long strained by Japanese atrocities during its 35-year colonial rule.

Both South Korea and Japan are ramping up defence spending and joint military exercises, which Yoon has said are essential for regional and global stability.

"There is an increasing need for Korea and Japan to cooperate in this time of a polycrisis with North Korean nuclear and missile threats escalating," Yoon said in a written interview with media ahead of his trip.

"We cannot afford to waste time while leaving strained Korea-Japan relations unattended. I believe we must end the vicious cycle of mutual hostility and work together to seek our two countries' common interests."

Seoul and Washington have ramped up defence cooperation in the face of growing military and nuclear threats from the North, which has conducted a series of increasingly provocative banned weapons tests in recent months.

On Tuesday, North Korea fired two short-range ballistic missiles, having launched two strategic cruise missiles from a submarine Sunday, just hours before the US-South Korea exercises kicked off. (AFP)