The council, which advises the government, is expected next week to recommend that ecstasy is downgraded from a class A drug to a class B one.
Ministers have outlined their opposition to any such move.
Professor Nutt wrote: "Drug harm can be equal to harms in other parts of life. There is not much difference between horse-riding and ecstasy."
The professor 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.
The ACMD last night distanced itself from Prof Nutt's comments.
A spokesman for the body said: "The recent article by Professor David Nutt published in the Journal of Psychopharmacology was done in respect of his academic work and not as chair of the ACMD.
"Professor Nutt's academic work does not prejudice that which he conducts as chair of the ACMD."
'No safe dose'
David Raynes, of the National Drug Prevention Alliance, told the Daily Telegraph: "He is entitled to his personal opinion, but if his personal view conflicts so very strongly with his public duties, it would be honourable to consider his position. "If he does not, the home secretary should do it for him."
Last September a Home Office spokesman said the government believed ecstasy should remain a Class A drug. "Ecstasy can and does kill unpredictably. There is no such thing as a 'safe dose'," he said.