Government advisers have resigned in protest at the sacking of the chief adviser on drugs.

Two members of the Advisory Council on the Misuse of Drugs (ACMD) have stood down after home secretary Alan Johnson dismissed chairman Professor David Nutt for his vocal opposition of the government's policy.

Professor Nutt, writing in today's Times, predicted that "many others will follow suit" because "it seems unlikely that any 'true' scientist will be able to work for this, or future, home secretaries".

"My sacking has cast a huge shadow over the relationship of science to policy."

If a significant proportion of the 28-strong committee were to resign, he continued, the Home Office would "no longer have a functioning advisory group, which is very unfortunate given the ever-increasing problems of drugs and the emergence of new ones".

Professor Nutt has long argued that ecstasy and cannabis - class A and B drugs respectively - are not in the correct class and that all drugs should be ranked by a "harm" index. This, he says, would see alcohol ranked fifth in the harm index behind cocaine, heroin, barbiturates and methadone. Tobacco should rank ninth, ahead of cannabis, LSD and ecstasy.

His views were given a lot of coverage when he recently compared the 30 deaths a year that are linked to ecstasy and the 100 deaths a year from horse-riding accidents.

Johnson, writing in today's Guardian, has insisted that Professor Nutt "was not sacked for his views, which I respect but disagree with". The home secretary said the Imperial College professor "was asked to go because he cannot be both a government adviser and a campaigner against government policy".

Referring to Professor Nutt's comments about horse-riding, Johnson wrote in the Guardian: "There are not many kids in my constituency in danger of falling off a horse - there are thousands at risk of being sucked into a world of hopeless despair through drug addiction."

Pharmacist Marion Walker and Dr Les King, a former head of the Forensic Science Service's drugs intelligence unit, are the two council members who have already handed in their notice.

King said the government's attitude to the panel had changed recently. "It's being asked to rubber stamp a pre-determined position," he said.

King has backed Professor Nutt's calls for the panel to be made truly independent from the government. Drugs "can be totally depoliticised" in the same way that the work of the National Institute for Health & Clinical Excellence (Nice) had been, said King.

"It's all about harm. It's a scientific issue," he said.

King pinpointed the government's changed attitude to the panel to 2002, when then home secretary David Blunkett wanted to downgrade the classification of cannabis, and his stance was supported by the council. "In that situation it was something that the council readily agreed to. That wasn't too worrisome but that precedent then continued," said King.

But former home secretary Charles Clarke has blamed the prime minister for reopening the issue of cannabis classification in 2007. "I think the mistake was right at the beginning of his premiership, saying he was going to change the cannabis rules before the advisory committee had considered its position. I think that was an error," he told the BBC.

Clarke called for ministers to reassure the scientific community that "their advice [and] their conclusions will be very seriously considered".