Tepco said on Tuesday that workers removed about 4,500 tons of the water from the tunnels linked to the No. 2 reactor building.
Underground space of the building is filled with highly contaminated water that had contact with melted nuclear fuel, raising concerns that the water could flow out to the nearby sea through the tunnels.
Since November, workers had been filling in the tunnels with cement to remove the water.
Officials say they hope to finish similar work at underground tunnels connected to the plant's No. 3 reactor in July.
The company estimates that more than 10,000 tons of such water has flowed into underground tunnels of both reactors.
In April last year, Tepco tried to create ice walls just outside the reactor buildings to keep tainted water out of the tunnels. But the plan did not work, and the utility decided to fill them with cement.
Tepco and the government say "they attach the highest priority to removing contaminated water from the tunnels, to avoid polluting the sea."