Police say Naddaf's charges could be upgraded to murder once forensic evidence from the home is analysed and the cause and time of death established.
"There are what appear to be stab wounds," Det Sen Const Berens said.
"Some of the stab wounds ... were still bleeding and suggest the injuries sustained were over a period of time and not all in one instance as the accused describes."
Brown's body was found at the couple's Craigieburn home on November 6.
Naddaf told police he woke up and found her tied up in the car by her legs, ankles and neck.
The prosecution says there were bloodstains throughout the house and in the garage.
Det Sen Const Berens says there's evidence that a "significant clean-up of the house" had taken place before authorities arrived.
Naddaf told police he untied his wife after he found her and carried her into the bedroom.
The 37-year-old, who has been in custody since his arrest, unsuccessfully applied for bail on Friday and will return to court in April.