The home secretary faces mass resignations from the government's drug advisory body over his decision to force out its chairman, who accused ministers of distorting scientific evidence on cannabis.

Two members of the Advisory Council on the Misuse of Drugs resigned yesterday in protest at Alan Johnson's treatment of Professor David Nutt. Another member told the Guardian that the experts were "planning collective action" against Johnson, adding: "Everybody is devastated. We're all considering our positions."

Nutt said there was "no future" for the council in its present form, and it is thought the group's members may use a meeting next Monday to announce a mass resignation.

In a letter in today's Guardian, Johnson accuses Nutt of "campaigning against government policy" but insists he was not forced out because of his opinions.

"Professor Nutt was not sacked for his views, which I respect but disagree with," he writes. "He was asked to go because he cannot be both a government adviser and a campaigner against government policy."

Scientists on the council are said to be preparing a letter to ministers seeking assurances that they will remain free to set their agenda and to speak freely about their research and findings.

The Times today reported that it was possible the 28 remaining members would quit if their concerns were not addressed before a council meeting next week.

The collapse of the panel, which provides ministers with evidence about the harm caused by different drugs, would be a severe embarrassment for the government and deal a heavy political blow to Johnson, who has so far steered clear of the controversies that dogged many of his predecessors at the Home Office.

As the row intensified yesterday, Nutt said he had been contacted by more than half the council's members, who had shared their "horror and disgust" over the manner of his dismissal and were now considering resigning en masse.

Dr Les King, a former head of drug intelligence at the Forensic Science Service, was first to act, followed by Marion Walker, the head of the substance misuse service at Berkshire NHS foundation trust.

King said he had decided to step down because he felt Johnson had denied Nutt his "freedom of expression".

He said that while the government had "a right" to reject the panel's advice, its attitude towards the advisory body had changed.

Nutt said he could "fully understand" why his two former colleagues had chosen to resign. "The government has interfered with the scientific processes of the panel for several years and it has caused significant resentment," he said.

"People are very much considering their positions and they have made it clear they will not continue under the current regime. There is no future for the Advisory [Council] on the Misuse of Drugs in the current way it operates."

Although Johnson would not comment on yesterday's resignations, he went on television to step up his attack on Nutt's conduct, insisting he had "crossed the line" with his remarks.

Charles Clarke, the former home secretary, said today: "The criticism of him [Nutt] is [that he was] campaigning. If that is the case, it was wrong. I cannot judge that."

Clarke argued that the system of classification was "trying to do too many things": not only classifying drugs according to the medical evidence, but also "sending messages about how people should behave in relation to drugs".

But he said the medical community had the right to complain about a government decision and to know that their advice was going to be listened to and "seriously considered".

And in another blow for Johnson, Lord Drayson, the science and innovation minister responsible for coordinating scientific advice across Whitehall, revealed yesterday that he was not consulted or informed by the secretary of state before Nutt's dismissal. Although he did not make any official comment, Drayson's Twitter account said he would be "asking why he was not informed, getting facts and finding a solution".

In an update this morning, he wrote that Johnson had "assured me of the importance both he and his department places on the academic freedom of advisers".

In an angry interview with Sky News yesterday, Johnson said: "You cannot have a chief adviser at the same time stepping into the public field and campaigning against government decisions. You can do one or the other; you can't do both."

Johnson said it was not the job of scientific advisers to "just keep coming back and back and back" to overturn ministerial decisions. He also stressed that the decision to force Nutt out had been his alone and he had not consulted the prime minister, Gordon Brown.

The home secretary said: "I've got enormous respect for the advisory council. I want to meet them very soon. I've got enormous respect for the scientific community. They've got to understand that Professor Nutt crossed this line between offering advice ... and then campaigning against the government on political decisions."

But Johnson found himself under fire from members of the scientific community. Lord Winston, the Labour peer and professor of science and society at Imperial College London, said he was "very surprised and disappointed" by Johnson's actions.

"I think that if governments appoint expert advice they shouldn't dismiss it so lightly," he said.

"I think it shows a rather poor understanding of the value of science."

The sacking follows the publication of a paper by the Centre for Crime and Justice at King's College London, based on a lecture Nutt delivered in July.

Nutt repeated his familiar view that illicit drugs should be classified according to the actual evidence of the harm they cause, and pointed out that alcohol and tobacco caused more harm than LSD, ecstasy and cannabis. Alcohol should come fifth behind cocaine, heroin, barbiturates and methadone. Tobacco should rank ninth, ahead of cannabis, LSD and ecstasy, he said. He also argued that smoking cannabis created only a "relatively small risk" of psychotic illness.

The Lib Dem science spokesman, Dr Evan Harris, who spoke to scientists over the weekend, accused Johnson of "political thuggery". He said the home secretary's actions could create a crisis in government policymaking if the drugs advisory panel was left unable to function or if experts on other panels resigned.

This morning David Cameron branded the row "unseemly".

"What seems to have happened here is the breakdown of confidence and mutual confidence between adviser and minister and some very unseemly scenes have followed," the Conservative leader said.

"But I am very clear in terms of the actual policy that we should not be changing classifications. We should be keeping them where we are, yes, on drugs, but also on alcohol."