Contaminated water remains the greatest challenge at Japan's Fukushima nuclear plant after the 2011 meltdown, the worst atomic disaster in a generation, the UN's nuclear watchdog said Tuesday.

"The crippled reactors are in a stable condition generally," International Atomic Energy Agency (IAEA) head Yukiya Amano told AFP while in the Slovak capital Bratislava.

"The most urgent priority is handling of the contaminated water," he said, after heavy rains caused a leak of radioactive water containing a cancer-causing isotope, possibly into the sea.

"It is also important to address the issue of decontamination of the off-site" so tens of thousands of evacuees can return home.

He spoke a day after Fukushima operator Tokyo Electric Power (TEPCO) said water contaminated with strontium-90 -- at 70 times the legal limit for safe disposal -- breached a barrier meant to contain radioactive overflow.

Strontium-90 is produced during nuclear reactions. It accumulates in bones and remains potent for many years, causing several types of cancer in humans.

On October 14, IAEA experts began a mission to assess clean-up efforts at the crippled Fukushima plant.

Amano said there will be another mission to Japan later this year to advise authorities on how to handle contaminated water.

TEPCO has poured thousands of tonnes of water onto badly-damaged reactors at Fukushima to keep them cool and prevent repeat meltdowns.

This huge volume of water must be stored in large tanks until it is clear of the radioactive substances picked up in the cooling process.

Threats of further contamination remain, Amano said, which include extreme weather, as Japan braces for a typhoon meteorologists say is likely hit later this week, bringing further rain to the country.