Public broadcaster NHK, citing government officials, said the isolated nation fired a projectile that appeared to be a ballistic missile.
Japanese Prime Minister Shinzo Abe has called for an emergency meeting of the National Security Council and told reporters that officials are analysing the launch.
He said: ‘I have received information that North Korea once again conducted a missile firing.
‘We will immediately analyse information and do our utmost to protect the safety of the Japanese people.’
His chief cabinet secretary Yoshihide Suga said the launch is a clear violation of United Nations resolutions, adding that Japan ‘absolutely cannot tolerate North Korea’s repeated provocations’.
He added that the missile flew for about 45 minutes and appeared to have landed in waters of the country’s exclusive economic zone.
There were no immediate reports of damage, but the coastguard has issued safety warnings to aircraft and ships.
The missile was filed shortly before midnight local time on Friday.
Navy Captain Jeff Davis, a spokesman for the Pentagon in the US, said: ‘We are assessing and will have more information soon.’