The plan, which still needs approval from the nuclear agency and local residents, comes as workers are locked in a daily struggle to safely store radioactive water used to cool reactors that went into meltdown after Japan's 2011 quake-tsunami disaster.
The tainted water is stored in hundreds of on-site tanks but operator Tokyo Electric Power (TEPCO) has admitted that it's running out of space.
It is also fighting to contain contaminated groundwater around the plant from seeping into the ocean, more than three years after the worst atomic crisis in a generation.
"But we know we have to get an agreement from the relevant government authorities, the prefecture and local fishing unions," a company spokesman said.
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The firm says it would significantly cut down on the amount of tainted groundwater flowing under the plant, after announcing earlier this year that it was building an "ice wall" -- freezing the ground around the plant -- to staunch the flow.
But the firm has long faced criticism over delays in disclosing key information and for continued safety problems at the crippled facility.
Hisayo Takada from Greenpeace Japan questioned the plan's safety.
"I also wonder if TEPCO has a backup plan for the worst case scenario, such as the purification facility not working effectively," she said.
The plant's current purification system -- Advanced Liquid Processing System (ALPS) -- has been hit by a series of glitches since trial operations began last year.