About 2 million people in the provinces of Zhejiang, Jiangsu, Shandong, Anhui, Fujian, Hebei, Liaoning and Jilin as well as the city of Shanghai had been relocated, the ministry said.
Nearly 13,000 houses collapsed and some 119,000 were damaged, while 996,000 hectares of crops were affected by the typhoon.
Lekima landed at around 1:45 a.m. Saturday in the city of Wenling in eastern China's Zhejiang Province. It made a second landing at 8:50 p.m. Sunday on the coast of Qingdao in Shandong Province.
The typhoon, the ninth and strongest of the year, has left 48 dead and 21 missing in Zhejiang, Shandong and Anhui. Zhejiang was the worst hit as the typhoon made the first landing there, leaving 39 dead and nine missing.
Authorities have mobilized dramatic rescue and relief efforts, with firefighters, soldiers, policemen and government agency staff searching for those missing.
On Monday, the country allocated 300 million yuan (42.66 million U.S. dollars) to help with rescue and relief work in Zhejiang, Shandong and Jiangsu.