Rescuers discovered the three miners on Monday morning and they were quickly rushed to hospital.
The accident occurred at the licensed Dahao coal mine in Guizhou province on Saturday.
Thirty-nine were underground at the time of the flooding and 26 managed to escape immediately, leaving 13 workers trapped.
Rescuers had recovered six bodies but continued to search for four others who remained missing, Chinaview reported.
Across the country, rescuers are searching for three miners still trapped in the Jinyuan coal mine which caught on fire on Sunday.
The death toll has already reached 12 after 31 miners were trapped underground at the time of the blaze. Sixteen have been rescued so far, China Daily reported.
The Jinyuan coal mine is located in China's north-east Heilongjiang Province and produces 60,000 tons per annum.