NOW Magazine has filed a complaint with the Integrity Commissioner over controversies related to their March 31 cover, which featured an image of Rob Ford's head photo-shopped onto another man's nearly naked body.

The cover was accompanied by an article called "The Naked Truth about Rob Ford."

The magazine is claiming that the Mayor's office asked to have the magazine removed from all City of Toronto offices and facilities, infringing on the publication's right to freedom of expression.

Alice Klein, the editor of the magazine, said in a press release on Tuesday that NOW has solid evidence that "someone in the Mayor's office felt empowered to order the removal and disposal of all our newspapers from all city buildings and facilities including all libraries."

Initial reports said that Lorraine Pickett, a custodial service supervisor at city hall, sent out an email suggesting the Mayor's office demanded the magazine be removed from city buildings.

The magazine said the email was a "disturbing infringement on the right to free expression and speaks to a careless disregard for democracy in the highest office of city government.'

The Mayor's office has said the entire incident was a misunderstanding and that a staffer was upset about the magazine cover but never asked for it to be removed. Ford's spokesperson, Adrienne Batra, has said Ford responded to photo-shopped images with good humour.

Enzo DiMatteo, associate news editor at the magazine, said he believes there was some misunderstanding about what directive was actually given, but the proof is in the email sent. He said that perhaps the mayor underestimated the reaction.

"I think if we perhaps didn't have this email, they could say they were offended. Now it's essentially become a story about the mayor deciding to remove or censor the magazine as opposed to being offended by the images," he said at the time.

Coun. Shelley Carroll told CTV Toronto's Naomi Parness that she thought the magazine had crossed the line, but that the mayor does need to be more open.

Carroll suggested that perhaps the mayor could make peace with the media and start talking to them on a daily basis.

DiMatteo said he hopes it was the picture and not the written words in the article that caused the problem.

"If it was the words, we'd really have a problem. I mean, either way, I think we live in a society where different points of view should be tolerated."

NOW magazine is also claiming Ford used "discreditable conduct in treatment of a member of the public by abuse or bullying contact to intimidate NOW Magazine."