Officers made the discovery early this morning on Black Hills Road at Gisborne South.
The body was in a shallow grave about five metres from the road. It has been removed by the coroner.
Police say they were led to the scene by the man charged with the murder and rape of Ms Meagher.
Adrian Ernest Bayley was remanded at an out-of-sessions court hearing shortly before 3am that lasted only 90 seconds at St Kilda Road Police Station.
The bail justice told Bayley he should not be given bail given the seriousness of the charges against him.
She asked him whether he understood the charges, to which he replied a simple “yes”.
Asked whether he wanted the charges read to him, the accused said “no”.
The accused wore a blue T-shirt, jeans and red-and-black Nike runners and showed no emotion as he sat with his chin in his hand.
Police will allege Bayley raped and murdered Ms Meagher on the morning of September 22 in Brunswick.
He will appear at Melbourne Magistrates’ Court later today.
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