Lord Mayor of Melbourne Robert Doyle has quit amid sexual assault allegations, while a new report highlights a “culture of fear” at the council.

Two of Mr Doyle’s fellow councillors recently raised sexual harassment allegations against the now former mayor. He is also the subject of an investigation by Victoria's health department after a third woman accused him of harassment at a hospital event.

Mr Doyle issued a statement through his lawyer saying he feels he has been denied the principles of fair justice.

“Following allegations seven weeks ago, he [Mr Doyle] has been through a period which he feels has lacked a semblance of natural justice, where the burden of proof does not rest with proving guilt, but rather proving innocence,” Mr Ruskin said.

“He continues to strenuously deny the allegations made against him.”

Mr Doyle has reportedly been admitted to hospital “to begin his recovery”.

Meanwhile, a confidential survey of City of Melbourne staff has revealed claims of “a culture of fear and trying to survive” at the council, with one respondent reporting “people who feel protected by anti-bullying and harassment policy engage in profoundly sexual commentary and harassment”.

The triennial survey is designed to measure fraud and corruption awareness among council staff and had 796 respondents.

It has been listed on the agenda for scheduled council meeting this week.

Reports say the comments about sexual harassment and bullying do not refer to Cr Doyle or any other councillor's behaviour.

A strong majority of respondents said they are aware of proper reporting mechanisms for concerns of fraud or unethical conduct, though some staff expressed a lack of confidence in those reporting mechanisms.

“In this [organisation] it appears that rocking the boat is frowned upon and 'yes people' get the promotions,” one staff member said.

“To be honest, I don't have a lot of confidence that [the City of Melbourne] would follow up allegations,” another stated.