A spokeswoman from Tokyo Electric Power Co (TEPCO) told AFP that the leak was detected at part of the plant that processes contaminated water.
"We estimate that roughly 5.5 tonnes (5,500 litres) of water leaked" on Wednesday morning, but "there have been no significant changes" at posts monitoring radioactivity around the power station, she said.
Even so, TEPCO plans to remove soil from around the area that may have been contaminated, the spokeswoman said, without providing specific details on the location of the leaked water.
The Fukushima plant was wrecked by a huge earthquake and tsunami in 2011 that killed 18,000 people. It was one of the worst nuclear disasters in history.
The clean-up operation is expected to take decades, with the most dangerous part -- removing radioactive fuel and rubble from three stricken reactors -- yet to begin.
In August, Japan began gradually releasing into the Pacific Ocean 1.34 million tonnes of treated wastewater that has collected since the catastrophe, saying it is harmless and heavily diluted with seawater.
This view is backed by the United Nations atomic watchdog, but China and Russia have criticised the release and banned Japanese seafood imports.
Wednesday's leak took place at a facility which processes the water before most radioactive elements are filtered out at a different, advanced facility known as ALPS.
TEPCO said the leak from a vent was spotted by a worker who was cleaning the vent before operating the facility.
"Vents should be closed during cleaning, but this time they were open," the spokeswoman said.
In a separate incident, smoke and sparks were detected on Thursday at a fan of Tsuruga nuclear power plant, which is in the process of decommissioning.
"The situation was resolved immediately with no injury or leak of radioactive materials," a spokesman of the operator Japan Atomic Power told AFP.
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