Conducted between 2005-2013, it found that 16.1% of China's soil and 19.4% of its arable land showed contamination.
There is growing concern, both from the government and the public, that China's rapid industrialisation is causing irreparable damage to its environment.
The study took samples across an area of 6.3 million square kilometres, two-thirds of China's land area.
"The survey showed that it is hard to be optimistic about the state of soil nationwide," the ministry said in a statement on its website.
"Due to long periods of extensive industrial development and high pollutant emissions, some regions have suffered deteriorating land quality and serious soil pollution."
Because of the "grim situation", the state would implement measures including a "soil pollution plan" and better legislation.
Levels of pollution ranged from slight to severe.
About 82.8% of the polluted land was contaminated by inorganic materials, with levels noticeably higher than the previous survey between 1986 and 1990, Xinhua news agency quoted the report as saying.
"Pollution is severe in three major industrial zones, the Yangtze River Delta in east China, the Pearl River Delta in south China and the northeast corner that used to be a heavy industrial hub," the agency said.
The report had previously been classified as a state secret because of its sensitivity.
There is growing fear in China over the effect that modernisation has had on the country's air, water and soil.
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