Yu Yongwei added that the drop in output may be one of the largest since the central government reduced the total grain planting area in an attempt to restructure the agriculture sector.
Drought in China's grain- growing regions is another factor, Xinhua news agency said.
A second ministry official, Min Yaoliang, said farmers in grain-growing provinces may earn less this year because of low crop prices.
The central government will work to minimize losses caused by the drought, Min said.
It will also speed up agricultural infrastructure development in a move to increase its anti-disaster capacity.
Yu said the grain planting area of more than 100 million hectares is down more than 5 percent from last year.
However, the land used for high-yield wheat increased by 1.93 million hectares and high-quality rice accounts for 50 percent of the total rice planting area.
Min said that means progress has been made in adjusting the crop-growing mix.
Unlike grain, meat output is estimated to increase 5 percent.
The output of aquatic products will likely reach 42.7 million tons this year, up 3.6 percent over last year, Min said.
In the first eight months of this year, China's import and export volume of agricultural products totaled US$17.5 billion, up 32.2 percent over the same period last year.
The import volume increased by 49 percent, reaching US$7.3 billion.
Min said most of the agricultural products imported were high-quality products to meet the domestic demand for different types of products.
The cash income per capita in rural areas reached 1,013 yuan (US$122) in the first half of this year, up 1.8 percent over the same period last year.