The operator of Japan’s crippled nuclear plant halted an emergency operation Tuesday to pump thousands of gallons of radioactive water from a leaking underground storage pool after workers discovered that a similar pool, to which the water was being transferred, was also leaking.

At least three of seven underground chambers at the site are now seeping radioactive water, leaving the Tokyo Electric Power Company with few options on where to store the huge amounts of contaminated runoff from the makeshift cooling systems at the Fukushima Daiichi nuclear power plant.

Those systems were put in place after a large earthquake and tsunami damaged the plant’s regular cooling systems two years ago, causing fuel at three of its reactors to melt and prompting 160,000 people to evacuate their homes. Since then, the Tokyo Electric Power Company, or Tepco, has been flooding the damaged reactor cores to cool and stabilize the fuel.

But Tepco has struggled to find space to store the runoff water. It initially released what it said was low-level contaminated water into the Pacific Ocean, igniting furious criticism among neighbors and environmental activists. Traces of radioactive cesium were later found in bluefin tuna caught off the California coast.