An upstream dam collapsed in Paradise Valley in Guangxi Zhuang Autonomous Region triggering the flood, local officials said.
Rescuers have recovered eight bodies so far. The injured have been sent to a hospital in neighbouring Mengshan County.
Authorities are working to verify the number of people who went missing during the flood.
Ten rescuers, aided by two local residents, are searching for the missing.
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The downpours have left 116 people injured and affected 2.60 lakh others across five counties due to floods and landslides, Yan'an's vice mayor Yang Xiao said.
Yang said the city has not seen rain of this extent or duration since 1945, when authorities first began to record meteorological conditions.
The rain has caused 3,710 landslides and cut off traffic on more than 120 roads, with direct economic losses estimated to total 1.47 billion yuan (USd 236 million), state-run Xinhua news agency quoted Yang as saying.
Meanwhile, two people were killed and one went missing as typhoon Soulik has gradually weakened on its course to inlands, but heavy rain and strong winds will continue to pummel some parts of China, the National Meteorological Center (NMC) forecast today.
As typhoon Soulik, the seventh typhoon to hit Chinese mainland this year, moved to Jiangxi Province after landing in Fujian Province yesterday, the downpours in Fujian and Zhejiang will gradually ease today, the NMC said.
But in Jiangxi Province, where the typhoon currently stays, most parts will be hit by rainstorms, and some regions in Anhui and Hubei will also be affected, the NMC warned.
It has affected some eight lakh people in Fujian and 4.10 lakh people in Zhejiang.