The United States called Friday for an emergency meeting of the UN Security Council after North Korea fired at least one ballistic missile.
The missile launch came amid protests from Pyongyang against joint military drills by US and South Korean forces and the UN increasing sanctions against the country.
One missile was fired at 5:55 am Friday (2055 GMT Thursday) from the west of the country, and travelled around 800 kilometres across North Korean territory before landing in the sea, South Korea's Yonhap News Agency reported, citing Seoul's Joint Chiefs of Staff (JCS).
Around 22 minutes after the launch, radar signals picked up by the South Korean military indicated a likely second missile launched from the same location, Yonhap said.
That signal was lost shortly afterwards, indicating the missile may have exploded in flight, the report said.
"An analysis so far indicates it was a missile, but more examination is needed to verify the data," it quoted the JCS as saying.
The missiles were thought to be of the Rodong model, which has a range of 1,300 kilometres and can reach all of South Korea and some of Japan, the report said.
The missile that reached the sea "dropped into waters within the Japanese Air Defense Identification Zone," or ADIZ, the JCS said.
Japanese Prime Minister Shinzo Abe said the country "categorically condemns" the launch, and "will closely cooperate with the international community to deal resolutely" with it.
A Defence Ministry source declined to confirm whether the missile landed in the Japanese ADIZ, which requires all aircraft to contact Tokyo before they enter it. The zone, which Japan last expanded in 2010, reaches hundreds of miles from the Japanese shore.
"We are still analyzing details," the source said.
Tokyo's Foreign Ministry said it had lodged a formal protest with Pyongyang's embassy in China, North Korea's main diplomatic ally.
Tensions have increased on the peninsula since North Korea tested a nuclear device in January and a long-range rocket in February, prompting the UN Security Council to impose its strictest sanctions ever on North Korea.
The isolated regime on March 10 launched two short-range ballistic missiles into the sea, according to South Korean officials.
The previous day, Pyongyang's communist leader Kim Jong Un said the country had succeeded in making nuclear warheads small enough to be carried by its ballistic missiles, although some observers have doubted this.
North Korea has complained about the ongoing South Korean and US annual military manoeuvres, Key Resolve and Foal Eagle, which have been running since March 7.
The North says the drills are a rehearsal for invasion. It said Wednesday it would launch a pre-emptive attack if it saw any sign of an attempt to breach its boundaries.