Groups representing scientists are divided in their response to the new requirement that independent scientific advisers must not undermine the "mutual trust" they have with the government if they want to keep their jobs.
Lord Drayson, the science minister, released the final principles of scientific advice setting out the rules of engagement governing the two parties last week.
They were drawn up after the sacking last year of David Nutt, former head of the Advisory Committee on the Misuse of Drugs.
Although a contentious phrase included in the draft consultation document, calling for the government and scientific advisers to "work together to reach a shared position", was removed, another - that "government and its scientific advisers should not act to undermine mutual trust" - remains.
The inclusion of the phrase was condemned by the Campaign for Science and Engineering, Sense About Science and Evan Harris, the Liberal Democrat shadow science minister.
But the Royal Society chose not to take issue, describing the principles as a "good framework" for the provision of scientific advice.
There was reluctance among leading scientists to comment on the matter. John Krebs, chairman of the Royal Society's Science Policy Advisory Group, was among the signatories of a letter sent to the government by 40 eminent scientists in February, urging the removal of the phrase on the grounds that it was subjective. But he declined to comment after the publication of the final principles.
The letter, sent by the directors of CaSE and SAS to Lord Drayson and John Beddington, the chief scientific adviser, says that the inclusion of the "mutual trust" clause would leave independent advisers open to "arbitrary sanction" by ministers, even when they abide by the Code of Practice for Scientific Advisory Committees.
It warns: "Unless steps are taken to mitigate the inclusion of the 'mutual trust' point, the finalised principles will institutionalise the very situation we sought to guard against."
Lord Drayson said the phrase had remained because departmental scientific advisers and Professor Beddington thought it was an important aspect of the principles.