The latest round of heavy rain has disrupted the lives of more than 130,000 people and damaged more than 7,500 hectares of crops, Xinhua reported.
In Wanzhou district, northeast of Chongqing, floods have caused 227.8 million yuan ($31.5 million) worth of economic losses, state broadcaster CCTV said.
Videos on social media showed raging rivers in towns and cities, and people being evacuated through waist-deep water. One clip showed rescuers breaking through a window security mesh to reach people trapped in an apartment.
Xi demanded that authorities at all levels give top priority to ensuring the safety of people and property, and he called on the State Flood Control and Drought Relief Headquarters and the ministries of emergency management and water resources to improve their coordination and warnings, Xinhua reported.
The finance and emergency management ministries announced 320 million yuan in emergency funds to aid disaster relief, including for Chongqing.
The Ministry of Water Resources launched flood emergency responses for the Inner Mongolia region, and Liaoning, Jilin and Heilongjiang provinces, CCTV reported.
Heavy rain is expected in those areas on Wednesday, state media reported.