Donald Trump and Japan’s PM Shinzo Abe have vowed to increase pressure on North Korea after the regime launched a missile over Japan on Tuesday morning.

The Japanese prime minister denounced the launch as an “unprecedented and grave threat” to the country’s security. In a 40-minute phone call with the US president they agreed to call for an emergency meeting of the UN security council to discuss the situation.

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Officials in South Korea said the missile may have flown further than any other tested by North Korea. The test, one of the most provocative ever from the reclusive state, sent a clear message to Washington just weeks after Kim Jong-un threatened to target the US Pacific territory of Guam with similar intermediate-range missiles.

It also demonstrated the regime’s willingness to raise the diplomatic stakes by sending a missile directly over Japanese territory. Pyongyang has tested more powerful intercontinental ballistic missiles (ICBM) this year, but Tuesday’s launch followed a much flatter trajectory than those tests.

Trump said the US was “100% with Japan” and repeated his strong commitment to the defence of Japan, Abe said shortly after the call.

“The outrageous act of firing a missile over our country is an unprecedented, serious and grave threat and greatly damages regional peace and security,” Abe told reporters in Tokyo, adding that his government had protested to Pyongyang via the Japanese embassy in Beijing.

The missile was the third fired by North Korea to have passed over Japanese territory. The first was in 1998 and the second in 2009, although Pyongyang claims they were satellites.

Abe said Japan would “strongly call for increased pressure on North Korea in cooperation with the international community” via the security council.

Japan’s J-Alert warning system advised people across a large area of northern Japan to seek shelter. Japan’s self-defence forces did not attempt to shoot down the missile and there were no reports of damage from falling debris.

The public broadcaster NHK said the missile had been launched from a site near the North Korean capital, Pyongyang and passed over a sparsely populated area of Hokkaido just after 6am local time (10pm Monday British summer time). It broke into three parts and landed in the sea.