"Our decision was unduly based on media and political pressure."
He added: "As well as being extremely unhappy with how the ACMD operates, I am not prepared to continue to be part of a body which, as its main activity, works to facilitate the potential criminalisation of increasing numbers of young people."
Speaking later to the BBC, he criticised the way the Home Office addressed drugs as a criminal justice issue, rather than a public health or social impact issue.
The mephedrone decision "was seen as a quick fix so that the home secretary could be seen to be acting being tough on drugs before an election," he said.
He said drug policy in the UK needed to consider why young people were attracted to drugs, with intervention and prevention being crucial.
According to the ACMD website, his appointment was from 1 January 2008 to 31 December 2010.
Another member of the ACMD told the BBC that they felt "properly consulted" and there were at least four meetings where mephedrone was discussed by the council or its expert committees.
The member, who does not have a scientific background, said they "did not feel under the slightest pressure from politicians or the media" when it came to making the decision to recommend that mephedrone should be classified as a Class-B drug.
Mr Carlin's resignation comes just days after another adviser, Dr Polly Taylor, quit the ACMD for similar reasons.
Professor Nutt, who was sacked by Mr Johnson in October 2009, said he was not surprised by Mr Carlin's resignation.
"There's not been proper consideration given to the broader justice and political aspects of making a drug Class B and criminalising maybe tens of thousands of young people," he said.
"I'm not surprised that people think it's all been done for political reasons rather than scientific or health reasons."
The Home Office called Mr Carlin's resignation "regrettable".
A spokesman said: "However it does not impact on our plans to ban mephedrone and the other substances as soon as parliamentary time allows.
"The home secretary has full confidence in [chairman] Professor [Les] Iversen and the rest of the ACMD committee."
Welsh Secretary Peter Hain said the government was right to act and Mr Carlin could have still argued his case while remaining a council member.
"Up to 25 people are suspected of having died from this drug. And for the government not to have acted and to have rendered it illegal I think would have been grossly irresponsible."
Shadow home secretary Chris Grayling said the relationship between the government and the ACMD had become "utterly shambolic".
He said: "After all the chaos of the last few months, it finally looked as if Alan Johnson might be getting things back into shape again.
"The decision on mephedrone was the right one, but this latest resignation suggests pretty clearly that the home secretary has been completely unable to restore his relationship with the experts who advise him."
Liberal Democrat home affairs spokesman Chris Huhne said: "Once again, the government's contempt for expert advice has decimated the ACMD.
"There is no point having experts to advise on drugs if Labour is only interested in pandering to tabloid newspaper editors.
"The only way to restore science to the heart of drugs policy is to make the ACMD completely independent of government."
Mr Johnson will ban mephedrone and the other substances within weeks, following the advice of the ACMD.
Class-B drugs, which include cannabis and amphetamine sulphate, carry a maximum sentence of five years in prison for possession or 14 years for supply.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.