Japan's Prime Minister Shinzo Abe says his nation is facing a "serious and grave threat" after North Korea fired a missile over northern Japan this morning.

Key points: Japanese military did not attempt to shoot missile down

Japanese military did not attempt to shoot missile down Missile lands in sea off northern island of Hokkaido

Missile lands in sea off northern island of Hokkaido US says launch does not pose threat to North America

The missile was launched from near North Korean capital Pyongyang and flew about 2,700 kilometres, reaching an altitude of about 550km.

It flew over Japan's northernmost main island of Hokkaido before breaking into three pieces and falling into the sea about 1,180 km to the east of Japan.

Air raid warnings sounded in northern Japan as the missile approached, with people being warned to take shelter in basements.

North Korea has conducted dozens of ballistic missile tests under young leader Kim Jong-un, but firing projectiles over mainland Japan is rare.

"North Korea's reckless action is an unprecedented, serious and grave threat to our nation," Mr Abe said.

"We will make utmost efforts to firmly protect the lives of the people," he told reporters as he entered his office for emergency meetings.

Mr Abe later said he had spoken to US President Donald Trump and they had agreed to increase pressure on North Korea.

Mr Trump also said that the US was "100 per cent with Japan" and he showed a strong commitment to Tokyo's defence, Mr Abe told reporters.

South Korea's Yonhap news agency said top US and South Korean military officers had agreed to a strong response, including possible unspecified military measures.

A spokesman for the presidential Blue House in Seoul said South Korean fighter jets had conducted bombing drills after Pyongyang's launch.

Sorry, this video has expired Alarms sound in Hokkaido, Japan after North Korea's missile launch.

Japanese Defence Minister Itsunori Onodera said concerns over the country's national security had heightened, while chief Cabinet Secretary Yoshihide Suga said the launch was a clear violation of United Nations resolutions.

The Japanese military did not attempt to shoot down the missile.

The UN Security Council was due to hold an emergency meeting late on Tuesday to address the launch.

Australia ready to stand with Japan, Bishop says

Foreign Affairs Minister Julie Bishop called the launch a serious escalation in its provocative behaviour.

Ms Bishop said firing a missile over the territory of another nation was a "provocative, dangerous, destabilising and threatening act".

She emphasised Australia's focus on reducing tensions on the North Korean peninsula.

"North Korea is in breach of numerous UN Security Council resolutions and is acting illegally," Ms Bishop said.

"Australia and Japan are in close contact … We stand ready to support Japan at any time."

Pentagon says 'no threat to USA'

The Pentagon said it was gathering more information but the missile did not pose a threat to North America.

Japanese soldiers with a Patriot anti-missile battery on the outskirts of Tokyo. ( Reuters: Issei Kato )

"We can confirm that the missile launched by North Korea flew over Japan," Pentagon spokesman Colonel Robert Manning told reporters.

"North American Aerospace Defence Command [NORAD] determined the missile launch from North Korea did not pose a threat to North America."

US stock futures and Asian share markets tumbled on the news, with Japan's Nikkei share average falling to a near four-month low.

South Korea's Finance Ministry said it would monitor financial markets around the clock and act to stabilise markets if needed.

"Our view is that we need to fully prepare and make stern responses to manage risks at home and abroad," the Ministry said after a policy meeting with the Bank of Korea and financial regulators that was urgently called after the launch.

Launch coincides with military drills by US, South Korea

North Korea typically reacts with anger to US-South Korean military drills, which are happening now, often staging weapons tests and releasing threats to Seoul and Washington in its state-controlled media.

A former South Korean military official, who is now an analyst at Seoul's Institute for Far Eastern Studies, said the early flight data from today's launch suggested the missile was likely a Hwasong-12, a new intermediate-range missile that the North has recently threatened to fire toward the US Pacific territory of Guam.

Mr Trump has warned Pyongyang it would face "fire and fury" if it threatened the US by firing missiles near Guam.

Seoul commuters at a train station watch coverage of the latest North Korean missile launch. ( AP: Ahn Young-joon )

Today's launch came days after the North fired three short-range ballistic missiles into the sea and a month after its second flight test of an intercontinental ballistic missile, which analysts say could reach deep into the US mainland when perfected.

North Korea first fired a rocket over Japanese territory in August 1998. The last time a North Korean missile flew over Japan was in 2009.

The 1998 launch flew about 1,500 kilometres before landing in the Pacific Ocean. The North later said was a satellite launch.

North Korea flew another rocket over Japan again in April 2009 and said that, too, was carrying a satellite.

Sorry, this video has expired File footage of previous North Korea missile launches

More launches could be on the way

Today's launch was met with mild concern across much of Japan, according to Wall Street Journal reporter Peter Landers, who is based in Tokyo.

"People have to some extent gotten used to missile launches so frequently," he said.

"I would say the mood is not of huge concern but it is wearing on the mind and people are concerned for the long term that they could raise the threat and launch one that could land in Japan."

But one expert cautioned there could be more missile launches in the near future.

David Schmerler, a research associate from the James Martin Centre for Non-proliferation Studies in Monterery, California, said if the launch was a failed test of a longer-range system, North Korea may be quick to try again.

"If it was the Hwasong-12, they might have been trying to do a fuller test to show it can hit locations by Guam," he told ABC News Breakfast.

"They are launching longer systems. If this missile failed, I would suspect another missile test relatively soon."

He said the missile was launched from Soonan, close to Pyongyang, probably to demonstrate that a missile could be launched from anywhere in the country using a mobile launcher.

Map The missile was fired from Pyongyang and landed in waters off Hokkaido.

Reuters/AP