The flooding, caused by torrential weekend rains, struck 17 provincial areas, killed 95 people including 37 in Beijing, and left another 45 missing, the Ministry of Civil Affairs said, China's official Xinhua news agency reported.
The disaster has affected about 6.23 million people in 264 counties, forced the evacuation of about 567,000 residents, destroyed 29,000 houses and damaged another 55,000, Xinhua reported.
The dead in Beijing included 25 who drowned, six who were killed in structure collapses, one killed by lightning strike and five electrocuted, municipal officials said. The rains, the heaviest in 60 years, submerged some power supply facilities, causing blackouts in parts of the city.
In a special report, Xinhua said the loss of lives has raised questions about the capital's ability to cope with flooding, adding many roads in the city remained submerged under waist-deep water for hours Saturday. As of Monday, the Beijing-Hong Kong-Macao expressway had not reopened.
The disaster caused about $1.6 billion of damage in the capital, Xinhua said, adding Beijing local governments were updating damage figures.
Many area residents used blogs to blame the local for Beijing's poor drainage systems, Xinhua said.
The report said urban flooding has been a chronic problem in China, adding rainstorms and flooding this summer have wreaked havoc in many cities, including Shanghai, Guangzhou, Chongqing and Shenzhen. Experts said they believe the floods are largely the result of urbanization, with vast networks of roads and the elimination of greenbelts decreasing cities' ability to cope with heavy rain.
One expert said more than 80 percent of Beijing's roads are covered in impermeable materials, obstructing infiltration of the rainwater. Another said about half of the drainage networks in Beijing are filled with sediments as thick as up to 50 percent of the pipes' diameter.
Others said reconstruction of the drainage systems would be extremely difficult and expensive.
The Wall Street Journal said besides the criticism about Beijing's ability to cope with such disasters, some doubts had been expressed about the official death toll of 37 in a city that prides itself on its infrastructure.
The report said the extent of damage in areas outside the city, and comments from some Internet users about official disaster statistics, led to speculation that the death toll could be higher.
The Journal said some were asking how a city that spent billions for the 2008 Olympics could struggle in dealing with a thunderstorm.
China Daily quoted Beijing Mayor Guo Jinlong as saying the city has a combination of old and new infrastructure, indicating some of the areas hit by the disaster have poor drainage.
"We will continue to update our emergency plans, improve the construction of infrastructure facilities, upgrade our ability to mobilize rescue staff and promote people's safety awareness in the future," he said.