The Japanese government has warned its citizens to take shelter after North Korea fired a missile over the country.

It was launched from the Sunan district of Pyongyang, South Korea's military said.

The missile has flown over Japan, Japan's NHK television said, but the government is warning citizens to avoid touching anything that looks like debris, the Daily Mail reported.

It comes as North Korea threatened to nuke Japan and reduce the US "to ashes and darkness" in response to the latest sanctions imposed by the UN.

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"Japan can never tolerate this repeated provocative action by North Korea," Tokyo's government spokesman told reporters.

"We have strongly protested to the North, telling them the strong anger by the Japanese people and condemn with the strongest words possible."

At a hastily convened press conference, Japan's Chief Cabinet Secretary Yoshihide Suga called the launch an "excessive provocation."

The government was also convening a National Security Council Meeting at the Prime Minister's office, the country's Defense Ministry said.

The missile landed 2000km off the cape of Erimo in Hokkaido island at 7.06am local time.

South Korea's defence ministry said it probably travelled about 3700km and reached a maximum altitude of 770km after being launched near Pyongyang's airport.

The North also launched a ballistic missile from Sunan on August 29, which flew over Japan's Hokkaido island and landed in the Pacific.

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

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

Japanese chief cabinet secretary Yoshihide Suga said no missile fragments have yet been found on Japanese territory.

It comes as North Korea threatened to nuke Japan and reduce the US "to ashes and darkness" in response to the latest UN sanctions.

The UN Security Council imposed its eighth round of sanctions on the country over its banned missile and nuclear programmes.

The North Korean threat was issued via the North's state news agency as US defence officials said the regime has spent the past 48 hours moving mobile missile launchers and preparing fixed sites for launch.

Elsewhere analysts from Johns Hopkins University said Kim Jong-Un's regime appears to be readying its nuclear test site for more detonations after the explosion of what North Korea claims was a hydrogen bomb on September 3.

Analysts believed that North Korea's latest missile, the Hwasong-14 is capable of reaching most of the mainland US, and has already been fired over Japan.

Kim Jong-un's regime appears to be readying its nuclear test site for more detonations. Photo / AP
Kim Jong-un's regime appears to be readying its nuclear test site for more detonations. Photo / AP

A spokesman for the regime told news agency KCNA: "The army and people of the DPRK are unanimously demanding that the Yankees, chief culprit in cooking up the 'sanctions resolution', be beaten to death as a stick is fit for a rabid dog.

"There's limit to patience. Now is the time to annihilate the US imperialist aggressors. Let's reduce the US mainland into ashes and darkness.

"Let's vent our spite with mobilisation of all retaliation means which have been prepared 'til now. These are voices of the Korean army and people.

"Also heard in the DPRK are strong accusations against the Japs who have zealously joined in the US racket for sanctions.

"The behaviours of Japs, sworn enemy of the Korean nation, are enraging us. The wicked Japs should not be pardoned.

"A telling blow should be dealt to them who have not yet come to senses after the launch of our ICBM over the Japanese archipelago.

"The four islands of the archipelago should be sunken into the sea by the nuclear bomb of Juche. Japan is no longer needed to exist near us."

Juche is the North Korean ideology, which mixes Marxism and self-reliance.

Japan's chief cabinet secretary Yoshihide Suga called the regime's statement "outrageous", saying it "escalates tension in the region and is absolutely unacceptable".

Seoul's military carried out a ballistic missile drill of its own yesterday in the East Sea, Korea's name for the Sea of Japan, the Yonhap news agency reported.

In July, Pyongyang fired two intercontinental ballistic missiles that appeared to bring much of the US mainland into range.

It followed that up with an announcement it was planning to send a salvo of rockets towards the US Pacific territory of Guam, home to significant military facilities.

US President Donald Trump threatened it with "fire and fury", heightening fears of conflict.

The United Nations Security Council sanctions imposed on Monday are the strongest so far, banning the North's textile trade and imposing restrictions on shipments of oil products, among a series of other measures.

But analysts expect them to do little to dissuade Pyongyang, which says it needs nuclear weapons to defend itself against the threat of invasion by the US.