"The mayor has called for this campaign to be withdrawn from the city's network of advertising billboards," said a spokesman told AFP.
The adverts will nevertheless remain on privately owned billboards.
The controversial advert was shot by Italian photographer Oliviero Toscani, the man behind hard-hitting and equally controversial campaigns by the Benetton group.
"What a shame that the city of Milan has a mayor like Moratti," said Toscani.
Milan is the second city in Italy to display the ads for Italian clothing firm "No-l-ita", which feature the slogan "No" to anorexia underneath.
The campaign against anorexia has stirred a fierce debate in Italy.
In France, the advertising self-regulatory body (BVP) strongly advised billboard owners against displaying the ads.