Pro-marijuana groups praised the mayor's "honesty"
Posters carry a quote from Mr Bloomberg, who, when asked before he became mayor if he had ever smoked marijuana, said: "You bet I did. And I enjoyed it."
The Washington-based group behind the campaign, the National Organisation for the Reform of Marijuana Laws (NORML), says it is "respectfully urging" Mr Bloomberg to stop arresting and jailing people who smoke the drug.
But Mr Bloomberg said: "I'm not thrilled they are using my name.
"I suppose there is that First Amendment that gets in the way of me stopping it," he added, referring to the US Constitution's guarantee of freedom of speech.
Mr Bloomberg made the remark about marijuana to New York magazine last year.
Now, in a $500,000 campaign, his comments are to be emblazoned across bus shelters, telephone booths, billboards and a full-page advertisement in The New York Times.
The poster's slogan is: "It's NORML to Smoke Pot."
However, Mr Bloomberg said that all city laws on marijuana would continue to be enforced, no matter what he may have said in the past.
Website message
NORML also invites visitors to its website to email Mr Bloomberg.
Its suggested message is: "Thank you for being honest and candid about your own use and enjoyment of marijuana. It is truly refreshing to find a politician willing to talk about marijuana honestly.
"There are millions of us who live in this fine city who similarly enjoy marijuana, as well as millions of others who don't smoke, but who nonetheless oppose arresting responsible smokers. It is time our policies reflected that reality."
In May last year, the US Supreme Court ended a legal battle over the medical use of marijuana, ruling that there were no circumstances which could justify it.
Dulling effect
Sufferers of diseases such as Aids, cancer and multiple sclerosis have claimed that marijuana helps combat symptoms of their illnesses.
Last month, research published in The Journal of the American Medical Association showed that long-term marijuana use had a dulling effect on the brain - affecting memory and attention span.
The study analysed 51 long-term users, 51 shorter-term users, and 33 non-users.
However, it was not clear whether giving up the drug would help users to recover.