Fifty six miners were in the Nadu mine in the Guangxi Zhuang autonomous region when it was flooded at 3:30 p.m. local time (09:30 GMT) on Monday.
Seven of the men managed to escape almost immediately, and another 13 were rescued in an overnight operation.
The rescue team working at the scene has established contact with 12 of the trapped miners, and is trying to get drinking water and food to them.
"The lack of oxygen in the narrow mining tunnel would make it difficult for the exhausted miners to get out by themselves," the news agency cited a rescue worker as saying.
The Chinese coal mining industry is the world's most dangerous, with up to 7,000 miners killed every year. Earlier this month, at least 10 workers died when a coal mine was flooded in the northern Shanxi province.