But last night Professor Nutt, who is head of psychopharmacology at the University of Bristol, retaliated, accusing the Government of "misleading" the pubic in its messages about drugs and of "Luddite" tendencies.

He was backed by other senior scientists and politicians.

Colin Blakemore, professor of neuroscience at Oxford University and former chief executive of the Medical Research Council, said: "The Government cannot expect the experts who serve on its independent committees not to voice their concern if the advice they give is rejected even before it is published. "I worry that the dismissal of Professor Nutt will discourage academic and clinical experts from offering their knowledge and time to help the Government in the future."

Richard Garside, director of the Centre for Crime and Justice Studies at King's College London, where Professor Nutt made his comments, said: "I'm dismayed that the Home Secretary appears to believe that political calculation trumps honest and informed scientific opinion. The message is that, when it comes to the Home Office's relationship with the research community, honest researchers should be seen but not heard." He added it was "a bad day for science and for the cause of evidence-informed policy making".

Professor Nutt had become a thorn in the side of ministers with his criticisms of drugs policy. He clashed with former home secretary Jacqui Smith when he suggested ecstasy, which causes 30 deaths a year, was less dangerous than horse-riding, which causes 100 deaths a year. He also argued that, to prevent one episode of schizophrenia linked to cannabis use, it would be necessary to "stop 5,000 men aged 20 to 25 from ever using" the drug.

Most drugs experts believe his analysis is right. But ministers did not want to hear the truth or at least to be reminded of it repeatedly. The Home Secretary asked him to consider his position after a recent lecture in which attacked what he called the "artificial" separation of alcohol and tobacco from other, illegal, drugs. Last night Professor Nutt said he stood by his comments. "My view is policy should be based on evidence. It's a bit odd to make policy that goes in the face of evidence. The danger is they are misleading us. The scientific evidence is there: it's in all the reports we published. Our judgements about the classification of drugs like cannabis and ecstasy have been based on a great deal of very detailed scientific appraisal.

"Gordon Brown makes completely irrational statements about cannabis being 'lethal', which it is not. I'm not prepared to mislead the public about the harmfulness of drugs like cannabis and ecstasy. I think most scientists will see this as an example of the Luddite attitude of governments towards science."

He repeated his view that cannabis was "not that harmful" and that parents should be more worried about alcohol.

"The greatest concern to parents should be that their children do not get completely off their heads with alcohol because it can kill them ... and it leads them to do things which are very dangerous, such as to kill themselves or others in cars, get into fights, get raped, and engage in other activities which they regret subsequently. My view is that, if you want to reduce the harm to society from drugs, alcohol is the drug to target at present."

In a recent broadside, Professor Nutt accused Jacqui Smith, who oversaw the reclassification of cannabis from Class C to Class B, of "distorting and devaluing" scientific research. He said her decision to reclassify cannabis as a "precautionary step" sent mixed messages and undermined public faith in government science.

"I think we have to accept young people like to experiment – with drugs and other potentially harmful activities – and what we should be doing in all of this is to protect them from harm. We therefore have to provide more accurate and credible information. If you think that scaring kids will stop them using, you are probably wrong."

The Home Office said Mr Johnson had written to Professor Nutt expressing "surprise and disappointment" over his remarks. Mr Johnson said in the letter that Professor Nutt had gone beyond providing evidence to "lobbying" for changes to policy. He said: "As Home Secretary it is for me to make decisions, having received advice from the [Council] ... It is important that the Government's messages on drugs are clear and as an adviser you do nothing to undermine the public understanding of them ... I am afraid the manner in which you have acted runs contrary to your responsibilities."

The shadow Home Secretary Chris Grayling said: "This was an inevitable decision after his latest ill-judged contribution to the debate, but it is a sign of lack of focus at the Home Office that it didn't act sooner, given that he has done this before."

But Phil Willis, chairman of the Science and Technology Select Committee, said: "I am writing immediately to the Home Secretary to ask for clarification as to why Sir David Nutt has been relieved of duties as chair of the Advisory Council on Misuse of Drugs at a time when independent scientific advice to Government is essential. It is disturbing if an independent scientist should be removed for reporting sound scientific advice."

Claudia Rubin from Release – a national centre of expertise on drugs and drugs law – said the expert should not have been penalised. "It's a real shame and a real indictment of the Government's refusal to take any proper advice on this subject," she said.