Robert Doyle is "very flat" says a colleague, as former Premier Jeff Kennett claims the outgoing Melbourne Lord Mayor has been denied a presumption of innocence amid sexual misconduct claims.

Having strenuously denied allegations of harassment and indecent assault against three women, Doyle relinquished his public positions late yesterday from his hospital bed where he is being treated for stress-related conditions.

"I do not think he has been given the presumption of innocence," former Victorian Premier Jeff Kennett told ABC Radio today. "In fact, quite the reverse. He has been trialled publicly."

Acting Lord Mayor Arron Wood spoke to Doyle from hospital shortly before his resignation.

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"It was a difficult phone call and my sympathy is with him and his family," Wood told 3AW. "There was not a lot of life in his voice."

In December, Doyle, 64, faced claims of sexual harassment, indecent assault and misconduct, and stepped aside as mayor while Ian Freckleton QC launched an investigation.

A report was due at a council meeting today, but it won't be ready as the process is still underway, Wood said.

City of Melbourne chief executive Ben Rimmer defended the investigation. "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 of the media."

Doyle's departure will trigger a byelection, at a date to be determined by the VEC. The state Government says Doyle's role must be filled quickly. "There will need to be quite quickly a replacement lord mayor, so we can have that leadership at a local government level for our city of Melbourne," Deputy Premier James Merlino told 3AW.

Doyle has also quit as chairman of Melbourne Health.

His wife Emma Page Campbell said her husband - a "good and decent man" - was "on the brink of being broken".

"I am disappointed that Robert has been given no benefit of the presumption of innocence - a resort to foregone conclusions, and with none of the protections afforded even to those accused of the most horrible crimes."

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Melbourne councillor Tessa Sullivan quit over alleged inappropriate behaviour by Doyle towards her and another woman.

A third woman later claimed Doyle touched her leg under a table and made offensive remarks to her at a Melbourne Health awards ceremony in 2016.

- AAP