The launches came as the North issued a stern rebuke to Washington over an impasse at nuclear disarmament talks, warning that the Americans' attitude could "gravely" affect the continuing disablement of Pyongyang's atomic facilities.
The missile tests were part of routine training, South Korean presidential spokesman Lee Dong-kwan said, declining to give further details on the type of rockets fired. He told reporters Seoul was "closely monitoring the situation."
"I believe North Korea would also not want a strain in inter-Korean relations," Lee said.
South Korea's Yonhap news agency reported that North Korea launched three ship-to-ship missiles at around 10:30 a.m. (9:30 p.m. EST Thursday), citing unidentified government officials.
South Korea's Defense Ministry said it would not be commenting on the launches, which came a day after Seoul withdrew officials from a joint industrial zone with North Korea at Pyongyang's request.
That move was prompted by the North's anger over South Korean statements that any expansion of the project in the border city of Kaesong would only happen if the North resolved the international standoff over its nuclear weapons.
South Korean President Lee Myung-bak, a conservative who took office last month, had said he would take a harder policy line on the North - a change from a decade of liberal Seoul governments who avoided confrontation to maintain a "sunshine policy" of engagement.
South Korea also voted Thursday in favor of a resolution at the U.N. Human Rights Council that condemned human rights abuses in North Korea. The North rejects such allegations and argues they are part of U.S.-led efforts to overthrow the regime.
The North showed signs earlier this week it was preparing to test short-range missiles as part of routine training, Yonhap reported. The country declared a no-sailing zone off the coastal city of Nampo and placed a military boat equipped with anti-ship missiles on standby, according to the news agency.
The North regularly test fires missiles, and its long-range models are believed able to possibly reach as far as the western coast of the United States. The country conducted its first-and-only nuclear bomb test in October 2006, but it is not known to have a weapon design able to fit inside a missile warhead.
North Korea shut down its sole operating nuclear reactor and has taken steps to disable its main atomic facilities under a landmark disarmament-for-aid deal reached last year with the United States and other regional powers.
However, negotiations on further disarmament have hit an impasse over the North's pledge to give a full declaration of its nuclear programs.
North Korea has claimed it gave the U.S. a nuclear list in November, but Washington said the North never produced a "complete and correct" declaration that would address all its past atomic activity.
On Friday, the North blamed Washington for the deadlocked talks and warned it would slow ongoing disablement of its atomic facilities.
The North's Foreign Ministry said the country has done its best to clear U.S. suspicions that it pursued a uranium-based atomic bomb program and also transferred nuclear technology to Syria, but Washington has been sticking to its "wrong" claims.
Pyongyang has "never dreamed" of doing either, the ministry said in a statement carried by the North's official Korean Central News Agency, and "such things will not happen in the future too."
"The U.S. side is playing a poor trick to brand (the North) as a criminal at any cost in order to save its face," the North said. "Should the U.S. delay the settlement of the nuclear issue, persistently trying to cook up fictions, it will seriously affect the disabling of nuclear facilities."
South Korean Foreign Minister Yu Myung-hwan said at a news conference with U.S. Secretary of State Condoleezza Rice earlier this week in Washington that "time and patience is running out" at the nuclear talks.