Robert Doyle, 64, has been accused of sexually harassing three women, including an allegation that he touched a colleague’s breast.
Mr Doyle has repeatedly and strenuously denied the allegations.
The political veteran had been serving his third term as lord mayor of Australia’s second-biggest city.
Mr Doyle went on leave in December after another councillor, Tessa Sullivan, resigned, accusing Mr Doyle of groping her and making inappropriate comments.
Two more women, including another city councillor, later raised harassment allegations against Mr Doyle.
Mr Doyle said at the time that he was shocked by the accusations, describing them as “thoroughly abhorrent”.
Late on Sunday, Mr Doyle’s lawyer Nick Ruskin reiterated that his client maintained his innocence.
“He has been through a period which he feels has lacked any semblance of natural justice, where the burden of proof does not rest with proving guilt, but rather with proving innocence,” Mr Ruskin said on Sunday.
Mr Doyle has also resigned as chairman of a public healthcare company, Melbourne Health.
Melbourne City Council is investigating the allegations. (Courtesy BBC)