Pyongyang "fired one ICBM-class ballistic missile toward the east. It flew for about 66 minutes," chief government spokesman Hirokazu Matsuno told reporters.
He said the missile flew an estimated 900 kilometres (560 miles), reaching a maximum altitude of 5,700 kilometres, and is believed to have landed at 6:27 pm (0927 GMT).
Matsuno responded "yes", when asked if the missile may have had a lofted trajectory, and said that whether it used solid fuel would be analysed.
"This series of actions by North Korea threatens the peace and stability of Japan and the international community, and is absolutely unforgivable," Matsuno added.
He said Japan had lodged a protest through "diplomatic channels".
"The government will respond by coordinating closely with the international community including the US and South Korea through the ongoing G7 foreign ministerial meeting and the UN Security Council."
Japan's deputy defence minister Toshiro Ino earlier said the missile was expected to land about 200 kilometres west of Oshima island in northern Japan's Hokkaido.
Prime Minister Fumio Kishida said he had "instructed (officials) to provide information to the public and thoroughly check the safety situation".
"It is an escalating provocation against the international community as a whole, and naturally we severely lodged a protest against it," he added.
Last November, a missile fired by Pyongyang was also believed to have landed in Japan's EEZ as North Korea carried out an unprecedented volley of launches.
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