, already saddled with debts twice the size of its $5 trillion economy, faces blackouts to conserve energy after the disaster, possible credit downgrades and the government is discussing a temporary tax rise to fund relief work.
The stock market plunged over 6 percent and one economist put the cost of the disaster at between 14 trillion yen ($171 billion) and 15 trillion yen just to the quake-hit region.
Engineers and rescuers battled through the weekend to prevent a nuclear catastrophe and to care for the millions without power or water in its worst crisis since World War Two, after the earthquake and tsunami
that likely killed more than 10,000 people.
Kyodo news agency said 2,000 bodies had been found on the shores of Miyagi prefecture, which took the brunt of the tsunami.
The core container of the No. 3 reactor was intact after the explosion, the government said, but it warned those still in the 20-km (13-mile) evacuation zone to stay indoors. The plant operator, Tokyo Electric Power Co (TEPCO), said 11 people had been injured in the blast.
Jiji news agency said seven people, six of them soldiers, were missing.
A Japanese official said before the blast 22 people had been confirmed to have suffered radiation contamination and up to 190 may have been exposed. Workers in protective clothing used hand-held scanners to check people arriving at evacuation centers.
U.S. warships and planes helping with relief efforts moved away from the coast temporarily because of low-level radiation. The U.S. Seventh Fleet described the move as precautionary.
Almost 2 million households were without power in the north, the government said. There were about 1.4 million without running water.
The government had warned of a possible explosion at the No. 3 reactor because of the buildup of hydrogen in the building housing the reactor. TV images showed smoke rising from the Fukushima facility, 240 km (150 miles) north of Tokyo.
TEPCO had earlier halted injection of sea water into the reactor, resulting in a rise in radiation levels and pressure. The government had warned that an explosion was possible because of the buildup of hydrogen in the building housing the reactor.
An explosion blew the roof off the No. I reactor building on Saturday.
"I was having lunch at a restaurant when I saw the news of the explosion at unit 3," said Mikiko Amano, 55, who was at her home a few km from the plant. "It only raised my distrust in TEPCO... The company has been saying such a thing would not happen."
A badly wounded nation has seen whole villages and towns wiped off the map by a wall of water, triggering an international humanitarian effort of epic proportions.
Prime Minister Naoto Kan said the situation at the 40-year-old Fukushima nuclear plant
remained worrisome and that the authorities were doing their utmost to stop damage from spreading.
"We have rescued over 15,000 people and we are working to support them and others. We will do our utmost in rescue efforts again today," he said.
Officials confirmed on Sunday that three nuclear reactors north of Tokyo were at risk of overheating, raising fears of an uncontrolled radiation leak.
Engineers worked desperately to cool the fuel rods. If they fail, the containers that house the core could melt, or even explode, releasing radioactive material into the atmosphere.
DEATH TOLL "ABOVE 10,000"
Broadcaster NHK, quoting a police official, said more than 10,000 people may have been killed as the wall of water triggered by Friday's 8.9-magnitude quake surged across the coastline, reducing whole towns to rubble. It was the biggest to have hit the quake-prone country since it started keeping records 140 years ago.
"I would like to believe that there still are survivors," said Masaru Kudo, a soldier dispatched to Rikuzentakata, a nearly flattened town of 24,500 people in far-northern Iwate prefecture.
Kyodo said 80,000 people had been evacuated from a 20-km (12-mile) radius around the stricken nuclear plant, joining more than 450,000 other evacuees from quake and tsunami-hit areas in the northeast of the main island Honshu.
Some workers showed up on Monday at a factory in Kuji even though it had been destroyed. Asked why he was there, a young worker smoking a cigarette outside the skeletal remains said: "Because it's a work day."
"NOT ACCORDING TO THE BOOK"
The crisis now centers on the Fukushima Daiichi nuclear complex, where authorities said they had been forced to vent radioactive steam into the air to relieve reactor pressure.
The complex, which was due to be decommissioned in February but was given a new 10-year lease of life, was rocked by a first explosion on Saturday, which blew the roof off the No. 1 reactor building. The government had said further blasts would not necessarily damage the reactor vessels.
TEPCO said on Monday it had reported a rise in radiation levels at the complex to the government. On Sunday the level had risen slightly above what one is exposed to for a stomach X-ray, the company said.
Authorities had been pouring sea water in two of the reactors at the complex to cool them down.
Nuclear experts said it was probably the first time in the industry's 57-year history that sea water has been used in this way, a sign of how close Japan may be to a major accident.
"Injection of sea water into a core is an extreme measure," Mark Hibbs of the Carnegie Endowment for International Peace. "This is not according to the book."
The nuclear accident, the worst since Chernobyl in Soviet Ukraine in 1986, sparked criticism that authorities were ill-prepared and the threat that could pose to the country's nuclear power industry.
Thousands spent another freezing night huddled in blankets over heaters in emergency shelters along the northeastern coast, a scene of devastation after the quake sent a 10-meter (33-foot) wave surging through towns and cities in the Miyagi region, including its main coastal city of Sendai.
As the country returned to work on Monday, markets began estimating the huge economic cost, with Japanese stocks plunging over 6 percent and the yen falling against the dollar.
Hiromichi Shirakawa, chief economist for Japan at Credit Suisse said in a note to clients that the economic loss will likely be around 14-15 trillion yen just to the region hit by the quake and tsunami.
Even that would put it above the commonly accepted cost of the 1995 Kobe quake which killed 6,000 people.
The earthquake has forced many firms to suspend production and shares in some of Japan's biggest companies tumbled on Monday, with Toyota Corp dropping 7.5 percent. Shares in Australian-listed uranium miners also dived.
"When we talk about natural disasters, we tend to see an initial sharp drop in production ... then you tend to have a V-shaped rebound. But initially everyone underestimates the damage," said Michala Marcussen, head of global economics at Societe Generale.
Ratings agency Moody's said on Sunday the fiscal impact of the earthquake would be temporary and have a limited play on whether it would downgrade Japan's sovereign debt.
Risk modeling company AIR Worldwide said insured losses from the earthquake could reach nearly $35 billion.
The Bank of Japan will debate on Monday whether to ease monetary policy further, sources said. The central bank earlier offered a combined 15 trillion yen ($183 billion) to the banking system earlier in the day to soothe market jitters.
Finance Minister Yoshihiko Noda said authorities were closely watching the yen after the currency initially rallied on expectations of repatriations by insurers and others. The currency later reversed course in volatile trading.
The earthquake was the fifth most powerful to hit the world in the past century. It surpassed the Great Kanto quake of September 1, 1923, which had a magnitude of 7.9 and killed more than 140,000 people in the Tokyo area.