Prof Nutt was sacked after he criticised a decision to reclassify cannabis
Leading scientists have told the government its attempts to safeguard the independence of scientific advice might do more harm than good.
Scientists including the president of the Royal Society told the government "firmer principles" should be written into a proposed ministerial code.
The code was drafted after the sacking of drugs adviser Professor David Nutt.
Home Secretary Alan Johnson sacked the UK's chief drugs adviser for "crossing a line" into politics in October 2009.
Prof Nutt had criticised a government decision to reclassify cannabis, saying it was less harmful than alcohol and nicotine and claiming it had been upgraded to Class B for political reasons.
As a result of his sacking, several other advisers resigned and over 20 scientists called for ministers to sign up to a code of conduct to prevent political interference in the system of scientific advice.
In response, Science minister Lord Drayson published a set of principles in December - one of which stated that scientists and ministers should "work together to reach a shared position".
But in a submission to a government review, the group of scientists - which includes Lord Rees of Ludlow, President of the Royal Society - claimed this requirement encourages ministers to intervene.
Ministers also water down advice that might be uncomfortable or embarrassing, their letter said.
It added there was too great a use of legally-binding non-disclosure agreements which keeps scientific advice on public policy issues secret.
BBC science correspondent Pallab Ghosh said there was a feeling among the experts that ministers had forgotten the lessons of the BSE crisis.
They say that was the last time scientists and ministers worked together to reach a shared position, which wrongly assured the public infected beef was safe to eat.