"Let me be very clear, I will not tolerate this kind of completely unacceptable behaviour in our schools," he said in a statement.

"There will be an independent investigation into the staff member's conduct, and he has been immediately stood down while this takes place."

However, Australian Principals Federation president Julie Podbury said Mr Merlino's comments were "disappointing" given an investigation was under way about what happened prior to the incident.

"No one needs to be commenting when they don't know the full facts," she said.

"It's terribly disappointing he has leapt to comment without knowing the full facts. It's not helpful."

Ms Podbury said the only people who should be privy to details about what happened were the parents, the principal and the department.

"The workload of a principal is 60 to 70 hours a week on a good week. There is an enormous amount of push and pull from all different directions and when something abhorrent happens it's no one's position to jump to judge, jury and executioner before they know the full story," she said.

"The role of principal is incredibly difficult and the community needs to protect these people. It's hard enough to get people to take this job without this sort of reaction, which is not helpful."

The Age has been told the president of the school council supports Mr Warner and was attempting to contact Victoria's Department of Education and the Education Minister on Friday morning.

A petition to reinstate Mr Warner as principal, created by Manor Lakes parent Mark England, had garnered more than 2000 signatures.

"Steve has only been around for a couple of years, and he has just turned that school around," Mr England said.

"It's a high school and a primary school with over 2000 kids. It needed to be someone who had done it before with results ... he's come in and turned the school around."

"I will take my kids out of the school if he goes ... I've had parents call me yesterday. As soon as they saw it, they thought, 'We are going to lose Steve'," he said.

"I think a lot of parents are of the same opinion ... What we are trying to do is put our hand up and say, 'Yes, he's done this, let people investigate'. But these parents support Steve."

Police confirmed on Friday morning that they had been notified.

"Police are investigating after a report was made regarding the treatment of a student at a school in Wyndham Vale on January 31," a police spokeswoman said.

"It is yet to be determined if the nine-year-old boy was injured during the incident. The exact circumstances are being investigated."

Mr Warner started at Manor Lakes at the end of 2016. He previously worked at Footscray City Primary School, where he was the executive principal for five years.

Victorian Education Department policy stipulates that a teacher may take any reasonable action that is immediately required to restrain a student from acts of behaviour dangerous to other members of staff, the student or any other person.

A spokeswoman said: "The department is aware of this video, and has launched an investigation into this matter.

"All school staff are expected to uphold the department's values, and abide by [Victoria's] Child Safe Standards."

The boy's family has been approached for comment.