The launch was reported by South Korea's Joint Chiefs of Staff (JCS), according to Yonhap, who said they were fired early Wednesday from the Sunan area in Pyongyang, and flew some 550 kilometres (340 miles) before splashing into the East Sea, also known as the Sea of Japan.
The JCS condemned the launches as "acts of significant provocation" and a clear violation of UN Security Council resolutions.
Japan's defence ministry also recorded the launches.
"We are analysing details, but we estimated that they have fallen outside Japan's exclusive economic zone, east of the Korean Peninsula," it said in a tweet.
The launches are the latest in a series of weapons tests by Pyongyang, and come as Seoul and Washington ramp up defence cooperation in the face of soaring tensions with the North.
On Tuesday, they held the first Nuclear Consultative Group meeting in Seoul and announced an American nuclear submarine was making a port visit to Busan for the first time since 1981.
The move had been expected to trigger a strong response from North Korea, which baulks at having US nuclear assets deployed around the Korean peninsula.
The launches also come less than a week after North Korean leader Kim Jong Un personally oversaw the firing of the country's newest intercontinental ballistic missile, the solid-fuel Hwasong-18.
Diplomacy between Pyongyang and Seoul has stalled and Kim has called for ramping up weapons development, including tactical nukes.
In response Seoul and Washington have staged joint military exercises with advanced stealth jets and US strategic assets.
The launches also come as Washington confirmed Tuesday that a US soldier is believed to have been detained by North Korea after crossing the heavily fortified border.
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