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The court was told an application for bail could not be heard because the teenager was awaiting psychiatric assessment at the Banksia Hill youth detention centre.
He is facing multiple charges in relation to the incident last week at Atlantis Beach Baptist College in Two Rocks, about 70km north of Perth.
They include discharging a firearm to cause fear, possessing a prohibited weapon and unlawful act with intent to harm.
Prosecutor Brad Hollingsworth on Tuesday said it was “very likely” the boy would also be charged with at least two counts of the more serious offence of endangering the life, health or safety of others.
Flagging that any bail application was likely to be opposed, Hollingsworth said the prosecution case would include a transcript of a triple-zero call allegedly made by the former student.
Other material included communications between the boy and his friends, and statements provided by teachers involved in the incident.
Magistrate Alana Padmanabham remanded the teenager in custody.
He is set to undergo a psychiatric assessment on Wednesday morning and return to court later in the day for his bail application to be heard.
Police alleged that the boy used two rifles to shoot three rounds at the school from a car park while he was inside a vehicle.
The incident forced the school into lockdown as students and teachers hid in a storeroom.
Forensic officers were seen analysing two bullet holes about five metres apart on the side of a demountable classroom.
One was above an external doorway and the other was beside a window, in clear view across a 30-metre-wide grassed courtyard adjacent to the car park.
Body-worn camera footage showed officers called to the scene took the boy into custody without incident.
The shooting is understood to be the first of its kind in WA.