The research will focus on animal, crop and fish farming and its findings are expected to be published by the end of 2008, according to the state-owned newspaper China Daily.
More than 1,000 'clean' villages are also being developed as part of the rural pollution control campaign, Mr Fengtong told reporters.
These will have the capability to dispose of 90% of all household waste and sewage. The use of fertilisers and pesticides has also been reduced by 15-30%.
China uses more than 360kg of fertiliser per hectare of land every year - 3.3 times more than the US and 1.6 times more than the EU average - but only about a third of it is used effectively, ministers said.
Mr Fengtong said: 'To develop ecologically modern agriculture, a fundamental change to the farming production model and way of life is essential.'
Agriculture is the main source of pollution in China's major waterway, the Yangtze River.
A team of Swiss and Chinese scientists revealed last month that agriculture had caused the quantity of nitrogen in the river to double over the past 20 years.
More than 300m Chinese people living in rural areas are currently affected by unsafe water supplies according to Government figures.