Professor David Nutt, chairman of the Advisory Council on the Misuse of Drugs, attacked the decision to make cannabis a class B drug.
He accused former home secretary Jacqui Smith, who reclassified the drug, of “distorting and devaluing” scientific research.
Prof Nutt said smoking cannabis created only a “relatively small risk” of psychotic illness.
And he claimed advocates of moving ecstasy into class B from class A had “won the intellectual argument”.
All drugs, including alcohol and tobacco, should be ranked by a “harm” index, he said, with alcohol coming fifth behind cocaine, heroin, barbiturates, and methadone.
Tobacco should rank ninth, ahead of cannabis, LSD and ecstasy.
Prof Nutt said: “No one is suggesting that drugs are not harmful. The critical question is one of scale and degree.
“We need a full and open discussion of the evidence and a mature debate about what the drug laws are for - and whether they are doing their job.”
In a lecture and briefing paper for the Centre for Crime and Justice Studies at King’s College, London, Prof Nutt attacked what he called the “artificial” separation of alcohol and tobacco from other, illegal, drugs.
He also repeated his claim that the risks of taking ecstasy are no worse than riding a horse.
In his paper, entitled Estimating Drug Harms: A Risky Business?, Prof Nutt attacked the decision to increase penalties for supplying class C drugs.
The move to double the maximum prison sentence from seven to 14 years was taken as a “tit for tat” move when cannabis was downgraded, he said.
In recent years drug classification policy has become “quite complex and highly politicised”, he said.
The Advisory Council on the Misuse of Drugs (ACMD) review of cannabis classification, ordered in 2007, was the result of a “skunk scare”, he claimed.
Overall, cannabis use does not lead to major health problems, he said, and users of the drug faced a “relatively small” risk of getting a psychotic illness compared to the risks of smokers contracting lung cancer.
Ms Smith’s decision to reclassify it as a “precautionary step” sent mixed messages and undermined public faith in Government science, he said.
He added: “I think we have to accept young people like to experiment - with drugs and other potentially harmful activities - and what we should be doing in all of this is to protect them from harm at this stage of their lives.
“We therefore have to provide more accurate and credible information.
“If you think that scaring kids will stop them using, you are probably wrong.”
Shadow home affairs minister James Brokenshire said: “Rather than adding clarity to the debate on drug classification, Prof Nutt’s comments will add even more confusion.
“He criticises the precautionary principle to drug classification yet his comments regarding the emerging harms linked to ketamine use underscore why this is appropriate.
“Similarly, drugs aren’t necessarily taken in isolation and giving simple labels of levels of harm risk gives a false impression of the dangers - drugs like GBL can be lethal if taken in combination with alcohol.
“Rather than providing clearer evidence on the harms linked to illicit drugs, Prof Nutt is making an overtly political pitch and that isn’t helpful.”
A spokesman for the Advisory Council on the Misuse of Drugs (ACMD) said: “The lecture Prof Nutt gave at King’s College was in his academic capacity and was not in his role as chair of the ACMD.
“We acknowledge that the lecture has prompted further debate on the harms of drugs.
“The ACMD seeks to provide the best evidence-based advice on the classification and harms of drugs to ministers and Parliament who make decisions.”
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