The move is an attempt to stop tonnes of unpolluted groundwater flowing under the battered plant and mixing with water already there and laced with radioactive isotopes.
Dealing with the huge -- and growing -- amount of water at the tsunami-damaged plant is proving to be one of the biggest challenges for Tokyo Electric Power co (TEPCO), as it looks to clean up the mess after the worst nuclear disaster in a generation.
For the last month TEPCO has been pumping up groundwater on the hillside before it enters the plant site, and storing it in tanks.
Today, engineers started releasing that water after it satisfied quality tests more rigorous than those put in place by the Japanese government or by the United Nations, TEPCO said in a statement.
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The bypass got the green light after TEPCO pledged it would exceed normal safety standards.
"With the bypass system, we are able to reduce by up to 80 tonnes per day" the volume of water that becomes contaminated under the plant, a TEPCO spokesman said.
In a test of water samples taken on April 15, the readings for potentially dangerous isotopes, including caesium and tritium, passed its self-imposed operational rules which are stricter than the government regulations.
Meanwhile, thousands of gallons of contaminated water are still being stored at the sites, with no permanent solution so far agreed.