A man from the Perth suburb of Balga, accused of killing his parents in Victoria's north-east, has made a brief appearance in a Melbourne Court.

Ian David Thomas, 35, is facing two counts of murder over the deaths of William and Pauline Thomas at their Wangaratta home five days ago

It is alleged he killed his 65-year-old father and his 63-year-old mother some time between Sunday night and Monday morning.

Their bodies were discovered on Monday night after police went to check their welfare.

Both bodies were found in the same room of the house, but police would not specify where.

It is unclear how they died, though police said they had suffered "significant injuries".

Mr Thomas was arrested at Meredith, near Ballarat on Tuesday night.

The court heard it is the first time Thomas has been held in custody and he requires medication for anxiety.

He was remanded into custody and will face the Wangaratta Magistrates court in September.