The operator of Japan's crippled Fukushima nuclear plant has reported that four tonnes of rainwater contaminated with low levels of radiation leaked during an operation to transfer the water between tank holding areas.

Tokyo Electric Power Co, or Tepco, has been trying to contain contaminated water at the Fukushima site after it found 300 tonnes of radioactive water had leaked from a tank at the plant. Fukushima suffered triple nuclear meltdowns and hydrogen explosions after a March 2011 earthquake and tsunami.

Heavy rain during a recent typhoon flooded one of the tank holding areas where Tepco stores excess water flushed over damaged reactors to keep them cool, a spokesman said.

After tests last month showed the rainwater contained 160 becquerels per litre of radiation, a relatively low level, Tepco officials decided to transfer the water to another holding area for tanks, he said.

During the transfer a worker found the leak, which the company estimated to be 4 tonnes and was absorbed into the ground, the spokesman said.

The company faces the prospect of more heavy rain in the next few days as another storm approaches Japan from the south.

Tropical Depression Sepat is forecast to gain strength overnight and arrive in the vicinity of Fukushima by 1200 GMT on Wednesday, the U.S. Navy Joint Typhoon Warning Centre said.

Tepco has been pumping hundreds of tonnes of water a day over the Fukushima reactors to keep them cool and storing the radioactive wastewater in tanks above ground. In August, the utility said at least one of those hastily built tanks was leaking.

It has also found high levels of radiation just above the ground near other tanks, suggesting widespread structural problems with the tanks.

Tepco's stock, which was up in the morning, fell after the utility announced the latest problem with water storage, closing down 4.1 percent.

Earlier on Tuesday, Tepco said one of three units for injecting nitrogen into the damaged reactors shut down due to a worker mishandling the equipment, but was restarted later. Tepco injects nitrogen into the reactors to prevent explosions similar to those that rocked the site in the early days of the disaster.