Tokyo Electric Power (TEPCO) switched off its Advanced Liquid Processing System (ALPS) after workers discovered leaks "seeping" from a tank yesterday.
About eight litres (2.1 gallons) of tainted water is believed to have leaked out, a company spokesman said. He added there was no immediate safety risk as the water had been recovered.
The suspension came just six hours after the embattled operator switched back on two of three lines in the system, which cleans radiation-tainted water used to cool the reactors damaged by Japan's devastating 2011 quake-tsunami disaster.
TEPCO is struggling to handle a huge -- and growing -- volume of contaminated water at Fukushima following the quake-tsunami, which sparked the worst atomic crisis in a generation as well as sweeping away some 18,000 victims.
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Giant waves crashed into the plant, sparking reactor meltdowns and explosions. Cleaning up the shattered site is expected to take decades.
There are about 436,000 cubic metres of contaminated water stored at the site in about 1,200 purpose-built tanks.
They say it will pose a negligible risk to marine life or people, but local fishermen and neighbouring countries are fiercely opposed.