The fluid splashed onto the men when they accidentally removed a pipe connected to the system, Tokyo Electric Power (TEPCO) said.
"The water did not come into contact with their faces so there is a little possibility that the workers ingested" any of the water, a TEPCO spokeswoman said, adding there were five other workers present at the time.
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The system is designed to desalinate contaminated water once it has been treated to reduce its caesium content. It is then stored in tanks on the site.
Today's incident will do little to improve the commonly-held view that TEPCO is making a mess of cleaning up the world's worst nuclear accident for a quarter of a century.
Earlier this week it was revealed a worker had accidentally switched off power to pumps keeping broken reactors at a steady temperature.
A massive earthquake and tsunami in March 2011 destroyed the plant's cooling system and caused meltdowns in its reactors, sending large quantities of radioactive materials into the environment.
TEPCO workers poured thousands of tonnes of water onto the reactors to keep them cool, and continue to douse them.
This now-radioactive water is being stored in around 1,000 tanks, which have been the source of leaks recently. Some contaminated water has made its way into the sea, the company has admitted.
TEPCO has so far revealed no clear plan for the water stored on site, but experts have said that ultimately it will have to be dumped in the Pacific, once it has been scoured of the worst of its radioactive load.
But this suggestion faces opposition from fishermen, environmental groups and neighbouring countries.
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