The missiles lifted off from Kaechon, north of the capital Pyongyang, about 6.50am on Wednesday in a northeast direction and flew about 400km, South Korea's Joint Chiefs of Staff (JCS) said, without specifying how many were fired and where they landed.
"We strongly condemn North Korea's missile launch as a clear provocation that seriously threatens the peace and stability of the Korean peninsula," the JSC said in a statement, vowing overwhelming responses to any further provocations.
About 30 minutes after its first missile notice, Japan's coast guard said North Korea fired another ballistic missile.
Japanese Defence Minister Minoru Kihara said at least one of the missiles fell near the North's eastern inland coast and that the launches "cannot be tolerated".
The US Indo-Pacific Command said on X that it was aware of the launches and consulting closely with Seoul and Tokyo.
The North fired several short-range ballistic missiles last Thursday, the first such launch in more than two months, which it later described as a test of a new 600mm multiple launch rocket system.
South Korea's JCS has said the launch might have been to test the weapons for export to Russia, amid intensifying military cooperation between the two countries.
The United States, South Korea and Ukraine, among other countries, have accused Pyongyang of supplying rockets and missiles to Moscow for use in the war in Ukraine, in return for economic and other military assistance.
North Korean Foreign Minister Choe Son Hui, who is visiting Russia this week to attend conferences, met her counterpart Sergei Lavrov in Moscow on Tuesday and discussed ways to promote bilateral ties, the Russian foreign ministry said on its website.
Wednesday's missile launches also came days after the isolated country for the first time showed images of centrifuges that produce fuel for its nuclear bombs, as leader Kim Jong-un visited a uranium enrichment facility and called for more weapons-grade material to boost the arsenal.
