Scientific advisers and the Government have been warned not to "undermine mutual trust" in a new set of draft principles governing the relationship between the two.
The proposal has been criticised by Evan Harris, the Liberal Democrat Science Spokesman, who has labelled it an "astonishing" suggestion.
The principles were drafted by Lord Drayson, the Science Minister, to restore confidence in the scientific advisory system in the wake of David Nutt's sacking as drugs adviser. They cover trust, respect, independence, transparency and openness.
They note that scientific advisers should "respect the democratic mandate of the Government to take decisions" and "recognise that science is only part of the evidence that Government must consider in developing policy".
Lord Drayson said: "Ministers rely on scientific advice to develop sound policy, and the relationship between ministers and advisers is an important one."
The document says the Government and its scientific advisers should "work together to reach a shared position, and that neither should act to undermine mutual trust".
It stresses that advisers are "free to communicate relevant evidence and analysis, including when it is at odds with Government policy", and that scientific advisory bodies have the right to "engage with the media and public independently of the Government".
It adds that scientific advice "will be published unless there are overriding reasons (such as national security) for not doing so".
Concerns were also raised by Lord Krebs, principal of Jesus College, Oxford, and one of a group of 28 senior scientists who set out their own principles for the treatment of scientific advice after the Home Secretary sacked Professor Nutt for criticising government drugs policy.
He called on the Government to clarify what is meant by "working together to reach a shared position", adding that the phrasing "could give ministers a licence to interfere with or suppress advice".
The principles are now being consulted on.