Acting chief Toyoshi Fuketa expressed his opinion at a news conference on Wednesday.
Highly radioactive water flowing into tunnels at the Fukushima Daiichi plant is believed to be mixing with groundwater and leaking into the ocean.
Tokyo Electric Power Company initially planned to freeze some of the contaminated water to stop the flow and allow its removal.
Fuketa said work to freeze the water has been unsuccessful and there may be no choice but to fill the tunnels with concrete.
He said it is not desirable to keep radioactive substances within the plant, and liquefied radioactive substances worsen the situation.
Fuketa said it would be better to seal in the underground water with cement than allowing it to flow into the ocean.
He also said failure to stop the flow of contaminated underground water would prevent freezing of soil and creating a wall of ice.
Nuclear Regulation Authority officials are expected to discuss TEPCO's idea of plugging the tunnels with cement and removing the radioactive water.