It is not the first time the utility has shut down the system, which has been hit by a series of glitches since trial operations began a year ago.
"We don't know yet when we can resume operating the system as we have not detected the cause of the defect yet," a TEPCO spokeswoman said.
"But we still have room to store toxic water so there is no immediate concern."
TEPCO is struggling to handle a huge – and growing – volume of contaminated water at the tsunami-damaged plant. There are about 436,000 cubic metres of contaminated water stored at the site in about 1,200 purpose-built tanks.
Many experts say that at some point the water will have to be released into the sea after being scoured of the most harmful contaminants. They say it will pose a negligible risk to marine life or people, but local fishermen and neighbouring countries are fiercely opposed.