Tokyo Electric Power Co. Said some of the water is seeping over or around an underground barrier it created by injecting chemicals into the soil that solidified into a wall.
The latest problem involves underground water which has built up over the last month since the company began creating the chemical walls to stop leaks after it detected radiation spikes in water samples in May.
TEPCO spokesman Yoshikazu Nagai said the company was slow to deal with the underground water leaks because it was focusing on cooling the damaged reactors, which posed greater risks.
TEPCO has been repeatedly criticised for delays in handling and disclosing problems at the plant. Alarmed by the latest problem, a panel of officials from local towns and villages rushed to the plant today for an inspection, demanding TEPCO limit the impact on the sea.
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Japan's nuclear watchdog set up a separate special panel with TEPCO and met Friday to assess the water problem and discuss ways to resolve it.
TEPCO officials were unable to answer many of the watchdog officials' questions, including ones about the leaks' origin, their routes and how they can be plugged. They also acknowledged that they have neglected large amounts of highly contaminated water that has remained in maintenance trenches since the crisis, a risk also cited by the watchdog.
"It's a race against the clock," said Toyoshi Fuketa, a commissioner of the Nuclear Regulation Authority. "The top priority is to keep the water from escaping into the sea."
After a major leak a month after the meltdowns, TEPCO said it had contained the problem and denied further underground leaks into the ocean were occurring, although many experts suspected they were.
While the extent of sea contamination remains unknown, TEPCO has estimated that up to 40 trillion becquerels of radioactive tritium, a water soluble element that can affect DNA but is believed to be less dangerous than cesium or strontium, might have leaked into the sea over the past two years.