The discovery has forced officials to abandon their original plan to bring under control the No. 1 reactor at the Fukushima Daiichi plant, crippled by the March 11 earthquake and tsunami. That plan would have entailed cycling a more limited volume of water across uranium fuel believed to have gone into meltdown.
Despite the setback, Japanese nuclear safety officials and the plant's operator, Tokyo Electric Power (TEPCO), plan to stick to a target of stabilising the plant and bringing its reactors to a state of "cold shutdown" by January.
"We want to preserve the timetable, but at the same time we're going to have to change our approach," Goshi Hosono, an adviser to Prime Minister Naoto Kan, told a television talk show on Sunday.
Outside experts have questioned whether the initial timetable for Fukushima was too optimistic. The 9.0 earthquake and the tsunami that followed unleashed the worst nuclear accident since Chernobyl in Ukraine in 1986.
Tepco is scheduled to provide an update on progress on Tuesday. In a pair of television appearances on Sunday, Hosono said the government would announce its own timetable for recovery efforts at the same time.
Tepco is preparing to pay compensation to thousands of residents, farmers, fisherman and businesses for the disaster under a plan directed and partly funded by the government.
Kan has said Japan's government shares responsibility for the disaster after promoting nuclear power for decades. A government study published last December and made public on Sunday shows that officials had made a detailed analysis of tsunami risk to nuclear plants.
Also on Sunday, about 7,800 residents northwest of Fukushima began a new round of evacuations. The towns are outside the 30-km safety zone set by the government but stood in the path of the radioactive plume that took shape just after the crisis.
The 9.0 magnitude earthquake and ensuing 15-metre tsunami devastated Japan's northeastern coast, killing more than 15,000 people. A further 9,500 are still missing.
PROBLEMS WITH RADIOACTIVE WATER
The wider evacuations come after worrying details emerged about the state of the No. 1 reactor last week. Progress to bring the unit under control has been seen as a test case for how quickly work on three other damaged reactors can proceed.
Among the revelations: the fuel in the reactor had melted down after the earthquake and dropped to the bottom of the pressure vessel at the core. Officials now estimate that the fuel rods in the No. 1 reactor could have been exposed to the air for as long as 14 hours after the accident.
A reading taken by a robot on the first floor of the reactor building on Friday recorded 2,000 millisieverts per hour, a level permitting workers to stay in the vicinity for no longer than eight minutes.
In addition, the reactor's containment vessel has leaked large amounts of the water being piped in to cool the fuel.
On Saturday, a Tepco worker was able to peer into basement of the reactor building and saw it had filled to almost half its 11-metre height with radioactive water -- an estimated 3,000 tonnes, larger than an Olympic swimming pool.
Critics have said that pumping in large amounts of water -- more than 10,000 tonnes in No. 1 reactor alone -- puts both the groundwater and nearby Pacific at risk.
"We have a problem to face dealing with the water," Hosono said. "We have to think of this in terms of a big loop - taking the water out of the plant, cleaning it and then returning it to cool the reactor."
That marks a break with the previous plan to use a more conventional cooling system. Instead, Hidehiko Nishiyama, a spokesman for the Nuclear and Industrial Safety Agency, said new steps were being readied to treat and store radioactive water.
Among the major risks ahead, experts say, is the prospect of another hydrogen explosion like those believed to have destroyed parts of the buildings housing reactors No. 3 and No. 4.
Workers stepped up the flow of water into the No. 3 reactor on Saturday after concern about the heat still being generated by its fuel. Officials also remain worried about the structural integrity of the building in No. 4 that supports its fuel storage pool, an area that raised concern among U.S. officials.