The Department for Environment, Food and Rural Affairs is asking the scientific community for ideas about what it should be researching.
Lord Whitty, Defra science minister, launched the department's Horizon Scanning programme last week.
It is designed to "provide a means for others to challenge Defra's current policy approaches and assumptions, to look for weaknesses and analyse data in new ways".
It will also offer a route for commissioning work on areas not seen as current policy priorities.
The department's annual research budget is £140 million.
"The BSE inquiry and guidelines from the government's chief scientific adviser both identify horizon-scanning as an important part of anticipating issues likely to be important in the future," Lord Whitty said.
The programme will be managed by the Science Policy Research Unit at Sussex University.
In April, it is due to submit proposals to an external advisory panel chaired by Anna Bradley, director of the National Consumer Council, which will pass on recommendations to Defra.
Formerly the Ministry of Agriculture, Fisheries and Food, the department has come under severe criticism over the past decade for its handling of issues such as BSE and foot and mouth.
In December, it appointed a new chief scientific adviser, Howard Dalton, chairman of Warwick University's department of biological sciences.
Professor Dalton's appointment was at a higher grade than previous chief scientists in the departments to deal with the Defra's increased brief, which now includes the environment.
Peter Cotgreave, director of Save British Science, said that repeated cuts in Defra's internal science research budget meant that horizon scanning had not been happening, leaving the government totally exposed in the event of a crisis.
Dr Cotgreave praised Lord Whitty's initiative, but warned that the research budget was still too low.