South Korean officials, who initially called the reported launch "routine," later said there was no evidence it had occurred.
"We have information about the missile but we have no confirmation," Chief Cabinet Secretary Yasuo Fukuda told reporters. Japanese officials refused to disclose where they received the information, saying they were linked to security secrets.
A Defense Agency official also backtracked from an earlier announcement by the Japanese navy's top official that North Korea had fired a short-range missile. The agency only had information about a launch, and no confirmation, he said on condition of anonymity.
Earlier in the day, Japanese officials said North Korea fired a missile from the peninsula northwest coast into the Yellow Sea, although they said it posed no immediate security threat.
In Washington, before Japanese officials reversed course on the missile announcement, a Pentagon official confirmed the launch and said the United States also did not view it as a threat.
Japan last Friday launched two spy satellites into orbit to keep watch over the North's missile and nuclear programs, angering Pyongyang, which threatened to test-fire a missile.
The initial report Tuesday of a launch by North Korea added to growing fears in Japan that the reclusive communist state might take advantage of the war in Iraq to escalate its missile and nuclear development.
Earlier in the day, officials from Japan's Defense Agency and Transport Ministry said North Korea had fired a short-range missile, with a range of about 40 miles, from the northwestern coast of the Korean Peninsula.
Koichi Furusho, chief of staff of the Maritime Self-Defense Forces, Japan's navy, said it was likely a routine test. He played down the possible dangers and told reporters that his forces were not placed on any special alert.
But South Korea's Defense Ministry later cast doubt on the announcement, saying there was no evidence that North Korea had test-fired a missile.
"South Korean and U.S. military intelligence officials have checked on the report and concluded that there was no missile launch by North Korea," a ministry official said on customary condition of anonymity.
South Korea's new government, headed by President Roh Moo-hyun, has made strong efforts to reduce tensions with North Korea.
The U.S. military announced Tuesday that U.S. stealth fighter jets and other aircraft and troops currently in South Korea for joint war games will remain after the exercises are finished to act as a deterrent against North Korea.
In 1998, North Korea fired a long-range missile that flew over Japan and plunged into the Pacific Ocean. It is believed to possess missiles that could reach parts of the United States.
North Korea test-fired two short-range missiles in late February and early March amid tensions over its suspected nuclear weapons programs. Washington and South Korea have criticized the tests as attempts to force the United States into direct talks.
With the United States focused on the war in Iraq, some experts say North Korea might exploit the opportunity to test long-range missiles or reprocess spent nuclear fuel to make atomic bombs.
The Korean nuclear crisis flared last October, when U.S. officials said North Korea admitted having a nuclear program in violation of a 1994 agreement.
Washington and its allies suspended fuel shipments, and the North retaliated by expelling U.N. monitors, withdrawing from the Nuclear Nonproliferation Treaty and restarting a nuclear reactor.
By Yuri Kageyama