A children's court magistrate on Friday told the boy, 16, that police could use reasonable force to obtain his DNA if he resists.
The teen, who was appearing via video link, has been charged with murder after the remains of high school student Layla Jeffery were found in Donald, a small town in Victoria's rural west, on July 9.
She was reported missing four days earlier, triggering a large-scale bushland search involving local police, dog squad, air wing and search and rescue teams.
The 13-year-old's remains were found inside a home.
Police allege the accused was known to his teen victim.
The magistrate on Friday approved applications for police to physically examine and retrieve DNA from the 16-year-old after he formed a view there were "reasonable grounds" to believe the teen had "committed the offence".
Detectives found items at the alleged murder scene they believe came from the body of the person who committed the alleged murder and another they believe was carried by the victim at the time, he said.
Addresing the teen directly, the magistrate explained police will hand him an object and ask him to scrape the inside of his mouth.
"You have to do what the police ask," he said.
"If you don't, they can use reasonable force to obtain it."
"Alright," the accused replied.
He will return to court on September 10.
Layla was farewelled at a funeral on July 31, attended by mourners donning black hoodies and Hello Kitty accessories - her favourite clothes.
Her aunt Kaityn Cheyne remembered a "paradoxical" girl who disliked being perceived and liked to simply exist quietly alongside those she loved most.
"She was both shy and confident in many different ways; funny, sassy, kind, generous, stylish, sweet, cheeky, loving and considerate," she said.
Affectionately known as La-La or Laylabug to family and friends, she loved to climb things, spend time with her grandfather and motorbikes, and had begun taking an interest in fashion.
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