The disclosure of the meltdowns more than two months after the quake struck came as a U.N. nuclear safety team began an investigation into the worst nuclear disaster since Chernobyl, 25 years ago.
Experts are still trying to understand how events at the Fukushima Daiichi plant on Japan's Pacific coast, 240 km (150 miles) north of Tokyo, spiralled out of control after the earthquake and tsunami, which killed about 25,000 people.
"We're here to gather information and to seek to learn lessons, because the basis for the high standards in nuclear safety is never being complacent," said Michael Weightman, head of Britain's nuclear safety agency and leader of an 18-member International Atomic Energy Agency (IAEA) team.
Engineers are still battling to stop radiated water leaking from the reactors and bring the plant under control.
Representatives of the IAEA team, which includes nuclear safety experts from France, Russia, China and the United States, will meet Japanese officials this week before travelling to Fukushima.
The team from the U.N. agency will prepare a report that will be presented at a meeting of international officials next month in Vienna and represent the first outside audit of Japan's emergency response.
The plant's operator, Tokyo Electric Power Co, had been wary of using the term "meltdown" but said earlier on Tuesday it had concluded meltdowns had occurred at three of the six reactors.
The government and outside experts had already said that fuel rods at three of the reactors had likely melted soon after the disaster and the Tuesday disclosure confirmed what most outside experts had come to believe within days of the accident.
But the timing of the announcement renewed questions about whether officials had been forthcoming about the extent of the crisis, which spread fear of radiation contamination around the world.
"I think there was an element of the government's initial view of the accident that wasn't severe enough and that's something we have to reflect on," said Goshi Hosono, an aide to Prime Minister Naoto Kan, who has been coordinating the response to the accident.
Kan has come under fire for his government's response to the disaster and for what some say is patchy disclosure of information despite regular briefings.
"NOTHING IS RESOLVED"
In a report to the government, the utility also said the tsunami rather than the magnitude 9.0 quake had disabled external power and knocked out cooling systems, a point of keen interest in the quake-prone country, which relies on atomic power for about 30 percent of its electricity.
The radiation leaking from the plant is at much lower levels than it was in the days following a series of hydrogen explosions that came around the time of the meltdowns in March.
Some analysts said the delay in confirming the meltdowns suggested the utility feared touching off panic by disclosing the severity of the accident.
"The word 'meltdown' has such a strong connotation," said Sophia University professor Koichi Nakano. "Now people are used to the situation. Nothing is resolved, but normal business has resumed in places like Tokyo."
Tokyo Electric officials said damage to the No.2 reactor fuel rods had begun three days after the quake, with much of the fuel rods eventually melting and collecting at the bottom of the pressure vessel containing them. Fuel rods in the No.3 reactor were damaged by the afternoon of March 13, they said.
Hidehiko Nishiyama, a spokesman for the government's Nuclear and Industrial Safety Agency, echoed the utility's view that the 15-metre tsunami triggered the crisis but said a fuller picture would require an inspection of the site.
That process is likely to take months because of high radiation readings in areas of the plant, experts have said.
Tokyo Electric, better known as Tepco, has an interest in concluding that the quake did not cause the crisis since that could trigger a more costly review of power plants across Japan, said Sophia University's Nakano.
"It could very well be that Tepco is rushing to conclude that the tsunami is to blame to prevent further questions and give more momentum to the nuclear camp. It's not just Tepco, it's the whole nuclear industry, maybe business circles as a whole. It's highly political," he said.