Melbourne Lord Mayor Robert Doyle is facing accusations of sexual harassment.

Victoria's health department has started an investigation into Cr Doyle, who is also the chairman of the Melbourne Health board.

The investigation is over an alleged incident at a Melbourne Health function in 2016.

“Melbourne Health is supporting the family of a staff member since becoming aware of an incident at a 2016 function,” a spokesperson said.

“Robert Doyle has taken leave from his role at Melbourne Health.

“Melbourne Health is united against sexual harassment, assault or discrimination of any sort.”

It comes after two Melbourne councillors accused Cr Doyle of separate incidents of sexual harassment, indecent assault and misconduct.

The City of Melbourne has already ordered an investigation into those claims.

Cr Doyle has categorically denied all the allegations.

“As I have said previously, I strongly deny the suggestion that I behaved in an inappropriate manner,” he said.

“As these matters are being addressed within the confines of the investigation, it is not something on which I will comment further.”