The ministry said on Monday that the financial losses from Typhoon Hagibis two weeks ago had topped 1.1 billion dollars in 38 prefectures.
At least 8,500 agricultural facilities, such as reservoirs and drains, have been damaged. The estimated cost of the repairs is more than 440 million dollars.
The figure for rice, apples and other farm products is about 97 million dollars. The damage is spread over more than 14,000 hectares of farmland.
Forest roads, wood-processing plants and other forestry-related facilities sustained about 320 million dollars' worth of damage.
Fishing ports and fishery facilities have seen losses of about 88 million dollars.
Ministry officials estimate the total cost will rise further, especially in areas where rivers burst their banks.
Damage from Typhoon Faxai in September has reached 468 million dollars. The torrential rainfall last week has also caused extensive damage.