Alan Johnson has been accused by the Liberal Democrats of misleading MPs over the sacking of drugs adviser Professor David Nutt.
Lib Dem science spokesman Dr Evan Harris has written to the home secretary demanding an apology for alleged “slurs” against Prof Nutt.
Prof Nutt was fired for “campaigning” against government drugs policy.
It comes as science minister Lord Drayson backed calls for a new code of practice for scientific advisers.
Prof Nutt was controversially axed from his unpaid role as chairman of the Advisory Council on the Misuse of Drugs after using a lecture to say that cannabis was less harmful than alcohol and tobacco.
He also said it had been upgraded from class C to class B – against the council’s advice – for political reasons.
Mr Johnson has said Prof Nutt “crossed the line” in his role, by campaigning against government policy.
And Gordon Brown defended his removal, saying the government could not afford to send “mixed messages” on drug use.
In his formal letter of complaint, Dr Harris says the home secretary’s claim in a statement to MPs that Prof Nutt had started a debate on drugs policy in the national media “without prior notification to my department” was wrong.
He says the professor had discussed his paper with the Home Office’s chief scientific adviser before delivering a lecture on it – and that the lecture had even been advertised on the Home Office’s own website. It had not been attended by any media, he adds.
Furthermore, he says Mr Johnson’s claim that Prof Nutt had broken a code of practice for scientific advisers when he published a paper saying horse riding was more dangerous than taking ecstasy without approval was wrong and a “slur” on the professor’s character.
He also argues that Prof Nutt was an unpaid, part-time adviser and so not subject to the same rules as the government’s chief medical officer or chief scientific adviser, as Mr Johnson suggested in his statement.
And he disputes Mr Johnson’s claim that Professor Nutt had “campaigned” against government policy.
Dr Harris said: “Lord Drayson, the science minister, has now publicly criticised the home secretary for not consulting him over the matter and signalled that the government would endorse a code of practice for ministers under which Prof Nutt would still be in his position.”
He said he would be raising the issue in the Commons on Monday and demanding “urgent” action.
In an interview with The Times, Lord Drayson said the sacking of Professor Nutt had caused “serious concern” in the scientific community.
The minister refused to be drawn on whether Mr Johnson had been right to remove him as chairman of the Advisory Council on the Misuse of Drugs.
But he made clear that in future both he and the government’s chief scientific adviser, Professor John Beddington, should be consulted before any such action was taken against any other independent scientific adviser.
“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 told the newspaper.
“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.”
He refused to say whether he had considered resigning over the issue, saying only: “I think that questions like that should never be answered.”
But Lord Drayson did welcome proposals for a new set of principles for the treatment of independent scientific advice released on Thursday by a group of leading scientists.
The government would be publishing clarified guidance to ensure that scientific advice was kept free from political interference before Christmas, he added.