The home secretary, Alan Johnson, is facing growing anger from scientists and government advisers over his decision to force the resignation of his senior drug adviser, David Nutt.

Two other senior scientific advisers to the Home Office told Nutt they were "horrified" at his treatment. The former chairman of the Advisory Council on the Misuse of Drugs (ACMD) told the Guardian that Dr Michael Rodd, a specialist in computing who sits on the Home Office Science Advisory Committee, and Professor Sheila Bird, a Cambridge University statistics expert who sits on the same committee, had written to him privately saying "they were unhappy with the way the Home Office had dealt with my case". Neither could be reached for comment.

Other senior scientists and former government advisers also criticised Johnson today, arguing the episode would create a gulf between researchers and politicians and prevent the best scientists from offering their expertise to the government in future. "I thought it was an appalling decision and totally inappropriate," said Lord Krebs, a former Food Standards Agency chief, who has also led several independent scientific studies for government.

"It will send shockwaves through the scientific community and make it more difficult for the government to recruit the best people to help with scientific advice to underpin public policy."

If the government wanted to ignore scientific advice, he said, they should explain why. "Alan Johnson could have said, 'we hear what you say but the science is not yet sufficiently robust enough for us to take action'," said Krebs.

Krebs said he had spoken to many scientists and former government advisers over the weekend, and "not one person … has been other than horrified about it and feeling that this called into question the whole validity of the government's approach to independent scientific advice".

Michael Donmall, head of the National Drug Evidence Centre and a former member of ACMD, said: "No independent advisory council should be expected to rubber-stamp government policy decisions. This totally undermines the whole value and role of the advice … in this case it appears that government has neither heeded the advice of the ACMD, nor entered into an informed debate about the issues."

He added: "Sometimes it is necessary to be outspoken in order to bring public attention to the way it is possible for political expediency to run roughshod over expert advice."

Mark Walport, director of the Wellcome Trust and a member of the prime minister's Council for Science and Technology, said the episode risked alienating scientists and politicians.

"There's an important relationship of trust here – governments have to trust scientists to give their best possible advice and be conscientious, and, equally, scientists have to trust governments that their advice will be listened to and the interplay between them will be as transparent as possible," he said. "If that trust is lost, that would be a bad thing."

Nutt's sacking came days after the government supported the independence of scientific advisers in its official response to an inquiry by the House of Commons science and technology select committee on the use of scientific advice in government.

In its report, the committee said scientists should not be criticised for publishing scientific papers or making statements as professionals, independent of their role as government advisers, and that "it is important to safeguard the independence of the [science] advisory system. In situations where the independence of a [science advisory council] chairman or member is or might be threatened for political reasons, support should be offered by the DCSA [departmental chief scientific adviser] and/or the GCSA [government's chief scientific adviser]".

In response, the government said: "The committee can be assured that the GCSA will take steps to support [scientific advisers] should he believe that their independence is being impinged upon."

Sir David King, the former chief scientific adviser to the government, said Nutt had "stepped over the line" by criticising ministers' decision to go against his advice.

"It is fine for him to reassert the advice but it is a step further to criticise a minister for not taking it," said King.

"His advice was extremely sound and I wish the government had followed it but this has created a crisis in a way which is not being discussed in the media. I spent a lot of my time in government trying to recover public trust in the scientific community and all of this work could be undone by creating confrontation between scientists and ministers."

He added the home secretary should have let Nutt's criticism pass.

Lord Drayson, the science minister, has yet to comment officially on Nutt's dismissal but has expressed his concerns on Twitter. In a series of tweets over the weekend, he said Johnson had "assured me of the importance both he and his department places on the academic freedom of advisers [and] of the importance both he and his department places on the independence of the advice they provide".

His office said Drayson would be investigating the matter further on his return to the UK tomorrow. The minister also acknowledged the strength of feeling among scientists. "I recognise how seriously concerned the science community is by this."

Chris Gaskell, chairman of the science advisory council at the environment department, said the case served to "highlight the tensions that sometimes exist when advice is offered on the basis of scientific evidence and other evidence is taken into account".

Both sides needed to "understand and respect" each other, he said. "We are fairly clear what our role is. We advise, we don't make policy." Science evidence was "a very important component but often not the whole evidence base and therefore has to take its place" in the total evidence feeding into policy. But, he added, explanation should be given if particular evidence did not "hold sway".

Krebs said the sacking was surprising because, on the whole, the government listened to scientific advice. "On some occasions, contrary to what Alan Johnson says, I've heard ministers say I can't formulate the policy until the scientists have given me the answer. They'll hide behind science when it suits them," he said. "That makes this all the more shocking."