The move has stoked fears Pyongyang may be heading towards a nuclear test.
The White House called the missile launch, which has not been confirmed by Pyongyang, a bullying tactic and cast North Korea's Kim Jong-il as a cruel and untrustworthy leader.
The State Department said it was consulting closely with governments in the region about the incident, which came on the eve of a UN-hosted conference expected to focus on nuclear proliferation concerns, including North Korea.
White House Chief of Staff Andrew Card acknowledged "increasing evidence" that Pyongyang might be developing the capability to arm missiles with a nuclear bomb. But he said the United States believed North Korea was having little success in testing multistage rockets.
"It appears that there was a test of a short-range missile by the North Koreans and it landed in the Sea of Japan," Card told CNN's Late Edition.
"We're not surprised by this. The North Koreans have tested their missiles before."
Kyodo news agency, citing unnamed Japanese government sources, said the launch occurred around 2300 GMT on Saturday. It said the Japanese government believed the missile might have been a land-to-ship or small ballistic missile.
The missile, which had a likely range of around 100km, may have been launched from North Korea's east coast, Japanese state broadcaster NHK reported, quoting unnamed defence sources.
Pyongyang's nuclear programme
is shrouded in secrecy
Officials said the US military picked up indications that there was a test and contacted the Japanese government. US intelligence agencies are assessing the information to determine exactly what transpired.
A senior Bush administration official, who spoke on condition of anonymity, said the latest test followed an apparent missile test attempt on Friday that failed.
Card said: "They've had some failures ... We don't think they have had much success in their testing of all of these rockets, multistage rockets."
Kurtis Cooper, a State Department spokesman, said North Korea had conducted similar launches and that "such tests did not contradict North Korea's voluntary moratorium on ballistic missile tests".
But Democratic Senator Carl Levin of Michigan said it was troubling. "It's additional, very discouraging evidence that this administration's policy towards North Korea is failing," the senate armed services committee member said.
The incident comes amid what officials said were growing US concerns that North Korea might be trying to harvest nuclear material from a shut-down reactor and might be preparing for an underground nuclear test.
The US defence intelligence agency warned last week that North Korea had the ability to mount a nuclear device on a long-range missile and the communist state could hit US territory.
US President George Bush has urged North Korea to return to six-party talks aimed at ending the reclusive state's nuclear programme.
Pyongyang: Economic cohesion
between the two Koreas is crucial
North Korea says that the Bush administration's intentions are "hostile", and that the US is seeking to topple the Pyongyang government because it will not bend to its will.
In late 2003, North Korea said it would halt the manufacture of nuclear weapons if the US signed a non-aggression treaty. It also listed the establishment of diplomatic relations with the US, the guarantee of North Korea-Japan and inter-Korean economic cooperation, and the completion of light-water reactors as conditions.
The US rejected all North Korean demands.
The talks have been stalled for almost a year, and recent efforts to restart them have shown little progress.
North Korea has occasionally test-fired short-range missiles before. In 1998, it fired a long-range missile over Japan into the Pacific Ocean, stunning the Japanese government.
In March 2005, Pyongyang threatened to resume testing, saying it was no longer bound by a 1999 missile test moratorium to which it agreed when it was in talks with the United States.