Up until July 10, more than 505,000 homes had collapsed and 1.33 million houses had been damaged by floods that have mainly occurred in central, east and southern China since mid-May, the ministry said.
Economic losses nationwide have risen to 39.87 billion yuan (4.8 billion dollars).
The flooding has mainly occurred in two periods, the ministry said, the first being in mid-May when southern China, including Jiangxi, Fujian, Hunan, Guangdong, Guangxi and Guizhou provinces were hit by torrential rains.
Since June 20, those areas and five other provinces in central China, including Anhui, Henan and Jiangsu, which bound the central Huai River valley, have also been inundated by incessant storms.
More than 260 fatalities have occurred since June 20, where rains in southern Guizhou and in Chongqing municipality have sent torrents of water gushing down mountain passes, destroying homes and crops.
In the Huai River valley, the water levels have reached their highest in 10 years and the government has evacuated farming communities and blown up dykes in an attempt to reduce the amount of water in swelling rivers.
"In comparison to the same time last year, this year's flood disaster has been worse in the areas affected, fatalities, number of houses collapsed and economic losses," the ministry said.
"So far it has not reached the level of the big disaster of 1991 or the disaster of 1998," it said.
Some 4,150 people died in the 1998 floods, when huge stretches of the Yangtze River overflowed its banks, slamming rural communities throughout central-eastern China.