Three men have appeared in a Melbourne court charged over the murder of another man, who was allegedly raped by one of the accused.

Craig Levy 36, Ryan Smart, 37, and Jason Colton, 41, did not apply for bail when they faced Melbourne Magistrates' Court on Friday.

Levy and Smart were charged with murdering the man, who cannot be named for legal reasons, while Colton was charged with his rape and murder.

Colton allegedly used an "object" to rape the victim, court documents read.

The three accused are scheduled to return to court on March 22.

The man's body was found at a Brighton East home on Wednesday night, police said previously.

A friend of the victim, who has not been named for legal reasons, called Smart a "c***" and "f***ing asshole" when he appeared in the dock of the court.

The accused men and alleged victim, believed to be aged in his 30s, shared a house, Victoria Police said shortly after the body was found.