Glenn Fenwick, 59, appeared in Warrnambool Magistrates Court on Wednesday afternoon for a filing hearing.

The man was arrested by Victoria Police missing person squad detectives on Tuesday following raids at properties in Wangoom and Warrnambool.

On Wednesday he was charged with the alleged murder of Christopher Jarvis in 2006.

The 38-year-old was last seen when he left the house he shared with his partner and stepchildren on Warrne Road in Wangoom around 6am on Tuesday, June 13.

Mr Jarvis' family were in court for the filing hearing on Wednesday.

His son was asked to leave the courtroom after shouting the man had "murdered" his father, while his daughter pleaded with Mr Fenwick to "tell us where he is".

Mr Jarvis' daughter also told the accused man she hoped he'd enjoyed watching his own kids grow up.

Magistrate Simon Guthrie called for order in the court and said he understood the proceedings would be "distressing".

He remanded Mr Fenwick in custody until April next year and listed a number of custody management issues, including the man suffering an acquired brain injury and vascular issues requiring medication.

The magistrate ordered a hand-up brief be served on the defence by April 21.

The court heard it was not Mr Fenwick's first time in custody.

A 70-year-old Wangoom man and former police officer was also charged with murder late on Wednesday.

He will front the same court tomorrow.

The man had been transported to the Warrnambool Base Hospital for assessment early but was later cleared of serious medical issues.

Mr Jarvis was initially reported missing after he failed to arrive at work in June 2006.

Staff contacted his partner around 7.30am and his car - a silver 1991 Ford station wagon - was later located on fire at Warrnambool's Thunder Point about 8am.

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