Tokyo Electric Power Co. (TEPCO) put its Advanced Liquid Processing System (ALPS) on standby mode after it found processed water was cloudy instead of clear.
Higher-than-usual levels of calcium were believed to be the cause, but why the levels had become elevated was not known, a TEPCO spokesman said.
ALPS has three lines -- one of which has already been stopped for the same problem while the third is not functioning properly.
It is unknown when the company will switch the system back on, AFP reported.
ALPS is used to clean the radiation-tainted water that has been used to cool reactors at the Fukushima Daiichi plant, where Japan's devastating 2011 quake-tsunami disaster sparked meltdowns.
TEPCO has repeatedly switched the system off because of a series of glitches since trial operations began last year.
The utility is struggling to handle a huge -- and growing -- volume of contaminated water at Fukushima, the site of the worst atomic crisis in a generation.
Thousands of gallons of contaminated water are being stored on site, with no permanent solution so far agreed.