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North Korea has fired at least one long-range and two short-range ballistic missiles, said South Korea's Joint Chiefs of Staff (JCS).
Japan's Prime Minister Fumio Kishida says one may have been an intercontinental ballistic missile.
It comes after Pyongyang on Wednesday launched its most missiles in a single day - including one that landed near South Korea's territorial waters.
Seoul responded by firing three missiles of its own.
North Korea's multiple launches comes as the US and South Korea are staging their largest-ever joint air drills, which Pyongyang has strongly criticised as "aggressive and provocative".
The latest launch on Thursday morning led the Japanese government to issue a rare emergency alert to residents in some of its northern regions, telling them to stay indoors.
Tokyo initially said the missile had flown over Japan, but Defence Minister Yasukazu Hamada later said it did "not cross the Japanese archipelago, but disappeared over the Sea of Japan".
PM Kishida later condemned North Korea's "repeated missile launches", calling them an "outrage".
Meanwhile South Korea's Vice Foreign Minister Cho Hyun-dong and US Deputy Secretary of State Wendy Sherman said the launches were "deplorable, immoral" during a phone call on Thursday, according to South Korea.
It comes just a month after North Korea launched a ballistic missile over Japan - the first time it had done so in five years.
The North has tested a record number of missiles this year as tensions have risen.
Despite crippling sanctions, Pyongyang has conducted six nuclear tests between 2006 and 2017, and is believed to be planning a seventh. It has continued to advance its military capability - in breach of United Nations Security Council resolutions - to threaten its neighbours and potentially even bring the US mainland within striking range.
Wednesday's launch saw one of Pyongyang's ballistic missiles cross the Northern Limit Line (NLL), a disputed maritime border between the Koreas.
It landed outside South Korea's territorial waters but was is the closest a North Korean missile has come to the border.
Seoul responded with warplanes firing three air-to-ground missiles that also crossed the disputed maritime demarcation line.