The missiles lifted off from Pyongyang on Thursday morning AEST and travelled about 360km before plunging into the sea, the Joint Chiefs of Staff said, without specifying how many were fired.
"We strongly condemn North Korea's missile launch which is a clear provocation that seriously threatens peace and stability on the Korean peninsula," it said in a statement.
Japan's defence ministry said at least two ballistic missiles from North Korea flew more than 350km, to an altitude of about 100km.
Japanese Prime Minister Fumio Kishida, who last week visited Seoul to reconfirm ties with South Korea ahead of his upcoming resignation, said Tokyo strongly condemned the launch and lodged a protest against North Korea.
"We continue to make utmost efforts for monitoring and cooperate with the US and South Korea," Kishida said.
The suspected missile appeared to have landed outside Japan's exclusive economic zone and there had been no reports of damage, Japanese media reported.
North Korea last fired a missile on July 1, when it claimed to have successfully tested a new tactical ballistic missile capable of carrying a 4.5-ton super-large warhead.
The latest launch came days after North Korean leader Kim Jong-un pledged to produce "exponentially" more nuclear weapons and ensure they were ready for use "at any given time."
Kim late last month oversaw a test of an upgraded 240mm rocket launcher system which "proved its superiority in mobility and strike concentration". He also inspected new "suicide drones" and called for the development of artificial intelligence for unmanned vehicles.
North Korea has also been sending balloons carrying rubbish across the border into the south over the last few days, a campaign kicked off in May in retaliation for anti-Pyongyang leaflets flown into the country by South Korean activists.
North Korea faces accusations of supplying Russia with weapons including drones and ballistic missiles to be used in the war in Ukraine.
Ukraine and the United States, among other countries and independent analysts, say that Kim is helping Russia in the war by supplying rockets and missiles in return for economic and other military assistance from Moscow.
Moscow and Pyongyang have denied the accusations.
with AP
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