Authorities in Seoul said the missiles were fired in the space of less than an hour from the Sunan area in Pyongyang.
It comes just a day after US President Joe Biden left the region, following a trip that saw him vowing to bolster measures to deter North Korea.
North Korea has been test-firing a flurry of ballistic missiles since the beginning of this year.
Japan confirmed at least two launches happened on Wednesday but acknowledged there may have been more.
Japan’s Defence Minister Nobuo Kishi said first missile flew about 300km (186 miles) with a maximum altitude of around 550 km, while the second, reaching as high as 50 km, travelled around 750 km.
Mr Kishi criticised the launches, saying they were “not acceptable” adding that it would “threaten the peace, stability and safety of Japan and the international community”.
In a meeting convened after the missile launch, South Korea’s National Security Council called the test a “grave provocation”, the presidential office said.
The launches came hours after US President Joe Biden departed for the US on Tuesday evening, after a five-day trip that saw him visiting South Korea and Japan.
U.S. and South Korean officials had earlier warned that North Korea appeared ready for another weapons test, possibly during Biden’s visit.
During his visit to Seoul over the weekend, Mr Biden and his South Korean counterpart Yoon Suk-yeol agreed to hold bigger military drills and deploy more U.S. strategic assets if necessary to deter North Korea’s intensifying weapons tests.
Mr Biden had said the United States was “prepared for anything North Korea does.”
The timing of these launches is not an accident – just hours after President Biden completed his trip to Asia, and days after he agreed with South Korea’s president to bolster their defences against North Korea.
For weeks intelligence suggested North Korea was planning to test something major while the president was here. Slightly less provocatively, it has waited until he had left, but only just. Air Force One hadn’t touched down on US tarmac before the missiles were fired.
At their weekend summit, President Biden and President Yoon said they were ready to take on the threat of North Korea together. This was their first test. They have responded quickly, condemning the launches, while joint-firing missiles of their own.
This marks another escalation by North Korea, which, over the past six months has become increasingly aggressive. But the concern is over what comes next. Evidence is mounting that North Korea is preparing to test a nuclear weapon. This would be its first nuclear test in five years and a major step-up.
Missiles amidst Covid ’emergency’
The latest launches come as North Korea struggles to contain a suspected outbreak of Covid amongst its largely unvaccinated population of 25 million.
More than a million people have now been sickened by what Pyongyang is calling a “fever”, and more than 68 people have died since late April.
On May 12, North Korea test-fired ballistic missiles the same day that Mr Kim declared an “emergency” over the Covid outbreak.
South Korea has said it offered humanitarian aid, but Pyongyang is yet to respond.