Typhoon Utor made landfall Wednesday in Guangdong and has killed 33 people, with eight more missing in the province, China's state-run Xinhua news agency reported.
The typhoon has affected 8.37 million people and caused damage to houses and farmland, the ministry said.
In northeastern China, rain-triggered floods killed 72 people in Liaoning, Jilin and Heilongjiang provinces and left 103 people missing, the ministry said.
About 162,000 people were evacuated from flooded areas and 6,100 buildings collapsed for a total economic loss of about $1.39 billion, the Ministry of Civil Affairs said.
The ministry and the National Commission for Disaster Reduction said they have increased the emergency response level from VI to III.
Under level III response, a disaster zone team could be sent to the effected area within 24 hours and relief materials could be distributed within 48 hours, Xinhua reported.
The province has allocated $22.8 million in disaster relief funds to the region.