Typhoons, floods, landslides and hailstorms all battered China this year.
"Tropical storm Bilis caused 848 human deaths while typhoon Saomai took 483 lives," said a report from the ministry.
Bilis and Saomai fatalities accounted for 42.2 percent of the total death toll in natural calamities in 2006.
According to the report, eastern, southern and southwestern parts of China were the worst hit in 2006. Zhejiang, Fujian, Jiangxi, Hunan, Guangdong, Guangxi, Sichuan, Guizhou and Yunnan each reported over 100 human deaths.
"A total of 2,342 human deaths were reported in the nine provinces as a result of natural calamities in 2006, which is 74 percent of the national total," said the report.
It also noted that of the total death toll, 60 percent were men.