The operator of the leaking Fukushima nuclear plant said Tuesday that it dumped more than 1,000 tons of polluted water into the sea after a typhoon raked the facility.

Typhoon Man-yi smashed into Japan on Monday, bringing with it heavy rain that caused flooding in some parts of the country, including the ancient city of Kyoto.

The rain also lashed near the broken plant run by Tokyo Electric Power (TEPCO), swamping enclosure walls around clusters of water tanks containing toxic water that was used to cool broken reactors.

Some of the tanks were earlier found to be leaking contaminated water.

"Workers measured the radioactive levels of the water collected in the enclosure walls, pumping it back into tanks when the levels were high," said a TEPCO official.

"Once finding it was mostly rain water they released it from the enclosure, because there is a limit on how much water we can store."

The utility said about 1,130 tons of water with low levels of radiation -- below the 30 becquerels of strontium per litre safety limit imposed by Japanese authorities -- were released into the ground.

But the company also said at one site where water was found contaminated beyond the safety limit workers could not start the water pump quick enough in the torrential rain, and toxic water had leaked from the enclosure for several minutes.

Strontium is a potentially cancer-causing substance that accumulates in bones if consumed.

Thousands of tonnes of water that was poured on the reactors to tame meltdowns is being stored in temporary tanks at the plant, and TEPCO has so far revealed no clear plan for it.

The problem has been worsened by leaks in some of those tanks that are believed to have seeped into groundwater and run out to sea.

Separately, around 300 tonnes of mildly contaminated groundwater is entering the ocean every day having passed under the reactors, TEPCO says.