The pumping began early on Tuesday after a lengthy delay that state media said was caused by technical problems and lack of power to run the giant pumps brought in by rescuers.
There were no ambulances or medical personnel on hand at the Xinjing coalmine in Shanxi province, suggesting that rescuers did not expect to find any survivors from the flood, which appeared to be China's biggest mine disaster this year.
Li Yizhong, a senior Chinese work safety official, has accused the mine's managers of sending miners into a coal seam beyond its approved area. Other officials have accused managers of trying to cover up the accident.
Li Fuyuan, the mine manager, and at least eight other officials have been detained for questioning, although the mine's owner fled, state media reported.
The disaster in the country's dusty northern hill country highlighted the chaotic state of its coal mines, where about 6,000 miners are killed each year in fires, explosions and floods.