The blast occurred at reactor 2 at the Fukushima Daiichi plant, which engineers had been trying to stabilise after two other reactors exploded.
The protective chamber around the radioactive core of reactor 2 has been damaged and radiation levels near the plant have risen, officials say.
The crisis was sparked by a 9.0-magnitude quake and tsunami on Friday.
Thousands of people are believed to have died, and millions are spending a fourth night without water, food, electricity or gas. More than 500,000 people have been left homeless.
A fresh explosion rocked reactor 2 at the Fukushima Daiichi plant – 250km (155 miles) north-east of Tokyo – in the early hours of Tuesday.
Radiation levels around Fukushima for one hour’s exposure rose to eight times the legal limit for exposure in one year, said the plant’s operator, the Tokyo Electric Power Co (Tepco).
The radiation reading at 0831 local time (2331 GMT) climbed to 8,217 microsieverts an hour from 1,941 about 40 minutes earlier, Tepco said.
The annual legal limit is 1,000 microsieverts.
However, officials say that a level of one million microsieverts would be needed to cause widespread radiation sickness.
Some staff have been evacuated from the plant, but initial indications suggest it is not on the same scale as the previous blasts.
On Monday, a hydrogen blast at reactor 3 injured 11 people and destroyed the building surrounding it. That explosion was felt 40km (25 miles) away and sent a huge column of smoke into the air.
It followed a blast at reactor 1 on Saturday.
An explosion early Tuesday morning damaged the No. 2 reactor atJapan’s Fukushima Daiichi Nuclear Power Station, the third in a series of blasts that have now hit each of the three crippled reactors at the plant, plant officials said.
It was not immediately clear if the blast was caused by the buildup of hydrogen, as occurred at the two other reactors at Daiichi — one on Saturday and the most recent one on Monday, when there was also a large explosion at the No. 3 reactor. Some early reports in the Japanese news media suggested that the latest explosion amounted to a different and more critical problem than the previous two.
This explosion, reported to have occurred at 6:14 a.m., happened in the “pressure suppression room” in the cooling area of the reactor and inflicted some degree of damage on the pool of water used to cool the reactor, officials of Tokyo Electric Power said. But they did not say whether or not the blast had impacted the integrity of the steel containment structure that shields the nuclear fuel.