Alan Johnson was wrong to sack David Nutt as his chief drugs adviser without consulting government colleagues responsible for science policy, the Science and Innovation Minister said yesterday.

Lord Drayson told The Times that he could have warned the Home Secretary that the sacking would cause uproar among scientists, and that, in future, advisers should not be dismissed without his input.

His first public comments since Professor Nutt was sacked last Friday add to government divisions over the affair. Two members of the Advisory Council on the Misuse of Drugs (ACMD) resigned in protest at the sacking, and others demanded a meeting with Mr Johnson and assurances about their continued independence.

E-mails from Lord Drayson to No 10 at the weekend, when he was in Japan, have been leaked, which said the sacking was “a big mistake”. The spat between Lord Drayson and Mr Johnson will irritate Downing Street but is unlikely to be thought serious enough for Gordon Brown to take action against the Science Minister. A Government insider said Lord Drayson’s conduct was “uncollegiate”. Another said: “At the time Alan Johnson took this difficult decision, alongside all his other irresponsibilities, Lord Drayson was on holiday in Japan playing with motorcars, which would not have made it easy for the Home Secretary to run it all by him.”

Lord Drayson told The Times that the Government would endorse principles guaranteeing academic freedom to its expert advisers, that had been demanded by scientists in a letter to ministers. Details are still being examined, but he pledged to incorporate the principles into a clarification of the role of scientific advisers by Christmas.

Lord Drayson said Mr Johnson should have consulted him and Professor John Beddington, the Government Chief Scientific Adviser, before he sacked Professor Nutt for questioning Home Office rulings on the classification of cannabis and Ecstasy. Professor Beddington has backed Professor Nutt’s view that alcohol and cigarettes are more harmful than cannabis. Both Lord Drayson and Professor Beddington were abroad when the decision was made.The peer agreed that the affair had been unfortunate, “because it led to serious concern in the scientific community, and if I had been asked by the Home Secretary before he took that decision I would have said that a decision to dismiss Professor Nutt would have caused serious concern”.

He added: “It’s very important that in future the Chief Scientific Adviser and the Science Minister are consulted before ministers take decisions to sack independent scientific advisers.”

Lord Drayson would not be drawn on whether Mr Johnson had been right to sack Professor Nutt. “I don’t think it’s helpful to go around the loop again of a post mortem,” he said. “My focus is on how we go forward from this event.” Asked whether he had considered resigning over the issue, he said: “I think that questions like that should never be answered.”

Senior scientists, including 17 advisers, asked the Government on Thursday to agree to three principles so that academics were not discouraged from joining advisory bodies. They demanded that public discussion of scientific evidence that contravenes government policy should not be grounds for dismissal as an adviser; that membership of an official panel should not bar researchers from speaking freely; and that while ministers can reject advice they must explain why.

Asked whether the Government would endorse the statement, Lord Drayson said: “Yes. I think it’s really good. These ideas about how we can further clarify the rules of engagement between government and the scientific community are very helpful.”

Evan Harris, the Liberal Democrat science spokesman, who instigated the statement of principles, welcomed Lord Drayson’s endorsement. “Scientists still want recognition that the sacking itself was unjustified and Professor Nutt of course deserves an apology for the damage done to his reputation before a line can be drawn under this affair.”

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