Workers also found that the No. 1 unit's reactor building is flooded in the basement, reinforcing the suspicion that the containment vessel is damaged and leaking highly radioactive water.
The revelations are likely to force an overhaul of the six- to nine-month blueprint for bringing the reactors to a safe shutdown stage and end the release of radioactive materials. The original plan, announced in mid-April, was due to be revised May 17.
The operator, known as Tepco, said the No. 1 unit lost its reactor core 16 hours after the plant was struck by a magnitude-9 earthquake and a giant tsunami on the afternoon of March 11.
The pressure vessel a cylindrical steel container that holds nuclear fuel, "is likely to be damaged and leaking water at units Nos. 2 and 3," said Junichi Matsumoto, Tepco spokesman on nuclear issues, in a news briefing Sunday.
He also said there could be far less cooling water in the pressure vessels of Nos. 2 and 3, indicating there are holes at the bottom of these vessels, with thousands of tons of water pumped into these reactors mostly leaking out.
Tepco found the basement of the unit No. 1 reactor building flooded with 4.2 meters of water. It isn't clear where the water came from, but leaks are suspected in pipes running in and out of the containment vessel, a beaker-shaped steel structure that holds the pressure vessel.
The water flooding the basement is believed to be highly radioactive. Workers were unable to observe the flooding situation because of strong radiation coming out of the water, Tepco said.
A survey conducted by an unmanned robot Friday found radiation levels of 1,000 to 2,000 millisieverts per hour in some parts of the ground level of unit No. 1, a level that would be highly dangerous for any worker nearby. Japan has placed an annual allowable dosage limit of 250 millisieverts for workers.
The high level of radioactivity means even more challenges for Tepco's bid to set up a continuous cooling system that won't threaten radiation leaks into the environment.
Tepco separately released its analysis on the timeline of the meltdown at unit No. 1. According to the analysis, the reactor core, or the nuclear fuel, was exposed to the air within five hours after the plant was struck by the earthquake. The temperature inside the core reached 2,800 degrees Celsius in six hours, causing the fuel pellets to melt away rapidly.
Within 16 hours, the reactor core melted, dropped to the bottom of the pressure vessel and created a hole there. By then, an operation to pump water into the reactor was under way. This prevented the worst-case scenario, in which the overheating fuel would melt its way through the vessels and discharge large volumes of radiation outside.
The nuclear industry lacks a technical definition for a full meltdown, but the term is generally understood to mean that radioactive fuel has breached containment measures, resulting in a massive release of fuel.
"Without the injection of water [by fire trucks], a more disastrous event could have ensued," said Mr. Matsumoto.
Tepco also released its analysis of a hydrogen explosion that occurred at unit No. 4, despite the fact that the unit was in maintenance and that nuclear fuel stored in the storage pool was largely intact.
According to Tepco, hyrogen produced in the overheating of the reactor core at unit 3 flowed through a gas-treatment line and entered unit No. 4 because of a breakdown of valves. Hydrogen leaked from ducts in the second, third and fourth floors of the reactor building at unit No. 4 and ignited a massive explosion.