The embattled operator of the stricken Fukushima Daiichi facility said it had suspended the procedure just hours after it started because a new part was needed, adding that it did not know when it would resume.
Part of the system that absorbs radioactive caesium had reached its processing capacity and needed to be replaced far earlier than expected, TEPCO officials said.
The operation started at 8:00 pm (local time) yesterday and was stopped five hours later, said TEPCO, which had earlier expected the part to last for one month.
"We are studying the cause of this," said Junichi Matsumoto, TEPCO official in charge of nuclear operations.
TEPCO officials speculated that highly radioactive mud might have entered the treatment system or that waste water was more radioactive than previously measured.
"We do not have a firm timing as to when we can resume the operation of the water treatment facility," Matsumoto told a press conference.
TEPCO has struggled to cool overheating reactors at the plant, hit by a 9.0 magnitude earthquake and deadly tsunami on March 11.
The wave knocked out reactor cooling systems, sparking meltdowns, explosions and radiation leaks.
The world's worst nuclear accident since Chernobyl in 1986 has caused radioactive material to spew into the air, ground and sea and forced the evacuation of 80,000 people in a 20-kilometre (12-mile) radius.
Workers have pumped water into reactor cores and fuel rod pools, leaving more than 100,000 tonnes of contaminated water in basements, drains and ditches, some of which has leaked into the ocean.
The water must be decontaminated before it can be stored or recycled back through the reactors to cool them.
Pumping out the highly radioactive water should then allow workers to start longer-term repair work to the cooling systems.