Lord Mayor of Melbourne Robert Doyle has resigned seven weeks after allegations of sexual harassment were made against him.

Key points: Cr Robert Doyle has vigorously denied allegations of sexual harassment from two fellow councillors

Cr Robert Doyle has vigorously denied allegations of sexual harassment from two fellow councillors Cr Doyle's wife says the allegations have brought her husband to the "brink of being broken"

Cr Doyle's wife says the allegations have brought her husband to the "brink of being broken" He is currently in hospital seeking treatment

Two fellow councillors made the accusations late last year and a draft copy of a report into the claims of indecent assault, misconduct and sexual harassment, which was conducted by Ian Freckelton QC, was presented to Mr Doyle last week.

Mr Doyle has vigorously denied the allegations.

In a statement, his lawyer, Nick Ruskin, said Mr Doyle felt he has been denied the principles of fair justice during the City of Melbourne investigation.

"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."

On Friday it was announced the investigation into the allegations against Mr Doyle would be delayed as he grappled with serious health issues.

Mr Ruskin said Mr Doyle had since been admitted to hospital "to begin his recovery".

Acting Mayor Arron Wood said he spoke to Mr Doyle from hospital before the news was made public.

"He didn't sound good. He was calling me from hospital so obviously his health has suffered considerably and my sympathies are with his family," he told ABC Radio Melbourne.

"He didn't go into any great detail [about his health], just to say that things like high blood pressure and those sorts of things were on the cards, and that he'd been hospitalised as a result."

Mr Doyle, who has been mayor since 2008, also resigned from his position as chairman of Melbourne Health, following a separate investigation after a third woman accused him of harassment at a hospital event.

Doyle on the brink of being 'broken'

Mr Doyle's wife Emma Page Campbell said the allegations had brought him to "the brink of being broken".

Mr Doyle became lord mayor in November 2008. ( ABC News )

"I know my husband. I know his intentions, his character, his language, his manner," she said.

"None of the allegations against him accord with the man I know.

"I have watched one of the strongest men I know brought to the brink of being broken."

A City of Melbourne spokesperson said it had been informed of Mr Doyle's resignation late Sunday evening.

"The City of Melbourne understands, via the Lord Mayor's lawyers, that the formalities of his resignation will shortly be completed and we are now operating on that basis," the spokesperson said.

The city council said the investigation into the allegations would continue.

By-election to elect new mayor

A State Government spokesman said it would be inappropriate to comment further because the investigations were ongoing.

The Victorian Electoral Commission (VEC) will conduct a by-election to fill the position.

Mr Wood said he did not know when the vote would be held, but it would only be for the position of mayor and not the whole council.

Council CEO Ben Rimmer said the Minister for Local Government, Marlene Kairouz, and the VEC would be official notified shortly.

"We will provide further advice on the timing and process for (the) election of a new Lord Mayor once those details are confirmed with the commission," he said in a statement.

He defended the process and the presumption of innocence in completing the investigation.

"I will say that the investigation process commenced and was undertaken from a presumption of innocence, as it should," he said.

"The whole purpose of the investigation is to ascertain the facts of the allegations. I cannot control the behaviour of the parties or the media."

Melbourne councillors will meet on Tuesday for the first time this year to discuss the status of the investigation.

Former councillor Stephen Mayne said the council should release the full report into the investigation.

"I think it's probably now incumbent upon the council to actually release the full, final report so that everyone can see what the independent QC, an independent review process, has concluded," he said.