Liberal Democrat Home Office minister Norman Baker has resigned just days after his report advocating the legalisation of drugs was discarded without any consideration by Theresa May. The Home Secretary is believed to have been furious about the report – despite its scientific basis – and within minutes instructed officials to state that its findings would be ignored.

The report itself featured a foreword from May but its contents were commissioned by Baker. It contained research on the impact of drugs legalisation on public health and the criminal justice system.

Embarrassingly for May it showed that legalisation would have almost no negative impact on health or addiction levels. It even cited the advantages of freeing up the criminal justice system. It is well known that the Conservatives disagree with the Liberal Democrats on the issue, but the speed with which the report was binned outraged Baker.

Mr Baker accused the Conservatives of delaying the report’s publication because its findings could be politically embarrassing for them.

He told The Independent: “They have looked upon it as a Conservative department in a Conservative government, whereas in my view it’s a Coalition department in a Coalition government.

“That mindset has framed things, which means I have had to work very much harder to get things done even where they are what the Home Secretary agrees with and where it has been helpful for the Government and the department.

“There comes a point when you don’t want to carry on walking through mud and you want to release yourself from that.”

In his resignation letter to Nick Clegg, the deputy prime minister, Mr Baker said it had “been particularly challenging being the only Lib Dem in the Home Office”.

“I see a newspaper the other day likened [it] to being the only hippy at an Iron Maiden concert,” he wrote.

Mr Baker, formerly the transport minister, continued: ” In stark contrast to the Department for Transport, I regret that in the Home Office, the goodwill to work collegiately to take forward rational evidence-based policy has been in somewhat short supply.

“I have concluded, therefore, that for the time being at least, my time is better spent out of ministerial office.”

The Lib Dem MP also said his four and a half years in ministerial office had “squeezed the time available for my family and my outside interests, including my music”. Mr Baker is a part-time singer in a rock band.

In a written reply to the minister, Mr Clegg said he had done a “brilliant job” in Government and had “handled the political relationships within Government with great skill, always focussing on how to achieve liberal reform”.

He expressed regret at the loss of “one of the most effective ministers” in the Government but said he “fully” understood why he was stepping down.

Mr Baker’s move to the Home Office from Transport in October last year was highly controversial as the MP had previously written a book claiming that David Kelly was murdered and the security services then staged a cover-up.

But the Lib Dem leadership said they hoped it would “sharpen our campaigning edge” in a department where the two parties’ views were often at odds over issues of civil liberties.

Diana Johnson MP, Labour’s Shadow Home Office Minister, said the resignation was a sign of “more chaos at the Home Office”.

“Alongside the immigration shambles, the failed experiment of Police and Crime Commissioners and the failure to undertake basic checks into chairs of the child abuse inquiry, it’s clear Theresa May is losing control of her Department,” she said.

“As for the Lib Dems, this resignation has nothing to do with principle. They will be judged on their actions in Government where their record is one of failure having backed the Tories all the way. If it weren’t for their support and votes, nothing David Cameron and Theresa May have done would have been possible.”