A former police officer has faced court in Melbourne charged with nearly 100 offences including rape and stalking, allegedly committed on the job.

Brett Johnson, 41, is facing 98 charges over alleged incidents that occurred while he was on duty between 2010 and 2019.

Johnson appeared virtually in Melbourne Magistrates Court on Friday, turning on his camera briefly and waving to the magistrate from inside a car.

Dozens of charges allege he abused his position as a police officer, dating back to 2010.

It is also alleged he raped and indecently assaulted a woman in Greensborough in 2013.

He is facing the same charges over alleged incidents in Pyramid Hill in May and June 2015.

Johnson allegedly also stalked a woman in 2019, persistently contacting her on the phone and visiting her at home when not on police business.

Victoria Police said on Friday that Johnson, previously a leading senior constable, had resigned from the force.

He is due back in court in November.

-AAP