A "radicalised" teenager who was shot dead by police after stabbing a man in Perth on Saturday had physically assaulted another student at his school a week earlier.

The 16-year-old boy attacked a man in a car park in the southern suburb of Willetton and threatened police with a large kitchen knife before he was killed by a single shot fired by an officer.

Education Department director-general Lisa Rogers confirmed with the ABC that the Rossmoyne Senior High School student was suspended for several days following an altercation with another student last week.

"In this instance … he offended and well, he was suspended," she said.

"The school acted absolutely appropriately. Any offence on school site like that, we would expect a boy or a student to be to be disciplined."

Ms Rogers did not confirm any details of the assault other than it being physical.

When asked on ABC Radio Perth if he was deemed dangerous to other students earlier, the director-general referred the question to the police.

Boy charged over toilet incident

The Education Department on Monday confirmed the teenager had been involved in an incident in 2022 where students had set off a small explosion in an empty toilet stall.

Ms Rogers said the teenager and another student had thrown a lithium battery into a toilet.

Nobody was harmed and no major damage was caused to the school.

Ms Rogers said police investigated the incident and the boy had been charged and given a juvenile caution.

"It was the school that referred the boy to the federal police."

As a result, the boy had been enrolled into a Countering Violent Extremism (CVE) program.

"There was no indication at that point that he was at a risk in terms of an imminent threat to danger in the school," Ms Rogers said.

Rossmoyne Senior High School parents had previously made claims the boy had been using a school prayer space to spread extremist ideology, but Ms Rogers said there was no evidence of this.

She also denied claims made by other students that the teenager had been watching extremist content in class and attempting to share that content with other students using a USB stick.

"I've got absolutely no report of that," she said.

"Those classes are supervised he was closely monitored and supervised. What he did outside of the school gate, in regards to what he did with that content, I can't speak to. But I can tell you and I can assure parents that whilst that boy was at school, he was monitored."

On Tuesday morning, the premier, education minister and WA Police were dispelling reports of a fresh safety threat at Rossmoyne Senior High School.

Education Minister Tony Buti said messages were circulating purported to be from a student threatening harm to other students and staff.

WA police quickly confirmed the threats were "vexatious and were not made by the 'sender'".

"I'm very angry about the person that left those messages because what it did was it caused further concern for that community in regards to the school," Ms Rogers said.

"Let's be clear here -- we have a boy that has been radicalised and for a number of years now, that staff have worked really, really hard to make sure that boy was supported and indeed the school community was safe.