The missile flew over the northern island of Hokkaido before landing 2000 kilometres away in the Pacific Ocean, the Japanese national broadcaster NHK said.

It was fired eastward from the Sunan district in North Korea's capital, Pyongyang, South Korea's military said.

Japan did not attempt to shoot down the missile, which was launched at 6.57am, NHK reported.

"The government is advising people outside to take shelter immediately," NHK said earlier.

The South Korean and US militaries were analysing details of the launch, the South's Office of the Joint Chiefs of Staff said.

South Korea's presidential Blue House has called an urgent National Security Council meeting.

In July, North Korea fired two ICBMs on steep trajectories into the sea between the Korean peninsula and Japan. The regime said those launches put the entire US in its range.

North Korea conducted its sixth and most powerful nuclear test - of what is believed to have been a hydrogen bomb - on September 3.

The North has launched more than a dozen missiles this year as its leader Kim Jong-un seeks the capability to hit the continental US with an atomic weapon.

US President Donald Trump has said all options - including military - are on the table to stop North Korea from threatening the US.

The North previously launched a ballistic missile from Sunan on August 29; it flew over Japan's Hokkaido island and landed in the Pacific waters.

Yoshihide Suga, Japan's government spokesman, told reporters today's situation was similar to that of the August 29 test.

Japan protested against the launch in the strongest terms and said it would take appropriate and timely action at the United Nations and elsewhere, staying in close contact with the United States and South Korea, Suga told reporters.

North Korea had called that test a "meaningful prelude" to a threatened launch into waters near the US territory of Guam.

On Monday, the UN Security Council approved new sanctions against the North for its September 3 test after the US dropped key demands such as an oil embargo to win support from Russia and China, both of which can veto any proposals.

The resolution seeks to limit oil imports, ban textile exports and increase inspections of ships suspected of carrying cargo in breach of sanctions.

The North threatened to sink Japan and reduce the US to "ashes and darkness" for supporting the Security Council resolution.

The US dollar fell sharply against the safe-haven yen and Swiss franc in early Asian hours on Friday on reports of the missile launch, though losses were quickly pared back in very jittery trade.

The dollar sank over half a yen to as deep as 109.55 yen in a blink, before rebounding to 110.01.

The market has been braced for a missile test for some time, so the move by Pyongyang was no major surprise.