The man accused of killing Melbourne woman Jill Meagher is facing fresh rape charges over an alleged attack 13 years ago.

Adrian Ernest Bayley, 41, of Coburg, appeared via video link in the Melbourne Magistrates Court after being interviewed by police on Friday.

He is charged with the rape of a woman in Elwood, in Melbourne's east, in 2000.

Bayley is facing seven charges, including three counts of rape, threatening to kill, unlawful imprisonment and intentionally causing injury.

Police were granted permission yesterday to question Bayley and examine any distinguishing marks he may have.

Bayley's lawyers applied to the court to have the new charges suppressed, arguing it would prejudice the administration of justice and contaminate a jury in any possible trial in the case of Ms Meagher.

The court heard the case had received almost unprecedented levels of public scrutiny.

However, the magistrate refused to issue a non-publication order, ruling in the interests of open justice and reiterated Bayley is innocent until proven guilty.

Bayley will return to court on the new charges in April.

He is contesting murder and rape charges in relation to the death of Ms Meagher and will face a two-day committal hearing in March.