The panel is set to recommend downgrading ecstasy this week
The home secretary has told MPs she was "surprised" and "disappointed" by a drugs adviser likening the dangers of ecstasy to the dangers of horse riding.
Jacqui Smith said Prof David Nutt had "trivialised" the dangers of the drug.
She said she had told him he had gone beyond his role as head of the Advisory Council on Drugs Misuse.
Ms Smith said Prof Nutt had apologised, but he later defended his comparison, saying it had been "useful" in showing the risks associated with taking drugs.
'Not much difference'
The council, which advises the government, is expected later this week to recommend that ecstasy be downgraded from a class A drug to a class B one.
Ministers have outlined their opposition to any such move.
Professor Nutt's article, published in the Journal of Psychopharmacology last week, said: "Drug harm can be equal to harms in other parts of life. There is not much difference between horse-riding and ecstasy."
He said horse-riding accounted for more than 100 deaths a year, and went on: "This attitude raises the critical question of why society tolerates - indeed encourages - certain forms of potentially harmful behaviour but not others such as drug use."
Ecstasy use is linked to around 30 deaths a year, up from 10 a year in the early 1990s.
Fatalities are caused by massive organ failure from overheating or the effects of drinking too much water.
Speaking during Home Office questions in the House of Commons, Ms Smith said: "I've spoken to him this morning about his comments. I've told him that I was surprised and profoundly disappointed by the article reported."
She added: "I'm sure most people would simply not accept the link that he makes up in his article between horse riding and illegal drug taking.
"For me that makes light of a serious problem, trivialises the dangers of drugs, shows insensitivity to the families of victims of ecstasy and sends the wrong message to young people about the dangers of drugs."
Ms Smith also said: "I made clear to Professor Nutt that I felt his comments went beyond the scientific advice that I expect of him as the chair of the Advisory Council on the Misuse of Drugs.
"He apologised to me for his comments and I've asked him to apologise to the families of the victims of ecstasy."
However, Prof Nutt later said: "I was doing a statistical comparison. There is a view - and the home secretary takes this view - that you cannot make a comparison and it is misleading because some things are legal and other things are illegal."
He added: "I think there are a significant number of people who agree with me as well that these kinds of comparisons are useful."
The comparison was useful "so people who take drugs can understand what the risks were", he said.
Prof Nutt added: "I certainly didn't intend to cause offence to the victims of ecstasy or their families. One death is one too many."
Conservative MP Laurence Robertson said ecstasy "not only wrecks lives, and ends lives, but also fuels crime".
He argued that drug use and horse riding were "completely incomparable" and that Prof Nutt was in the "wrong job".
But, in questions to the House of Commons Speaker, Liberal Democrat MP Evan Harris said Prof Nutt was a "distinguished scientist" and asked whether it was "right to criticise him here when he cannot answer back for what is set out in a scientific publication".
He added: "What's the future for scientific independence if she [Ms Smith] asks that scientists apologise for their views?"
Speaker Michael Martin replied that it was a "parliamentary privilege" for the home secretary to make such remarks and that "of course" she would be allowed to do so.
The Advisory Council on Drugs Misuse has distanced itself from the comments in Prof Nutt's article.