Violent threats have been made against the new principal of Punchbowl Boys’ High School, after his predecessor was ousted over failing to implement anti-radicalisation procedures.

Former principal Chris Griffiths and his deputy, Joumana Dennaoui were removed from their roles by the Education Department over “disunity and disharmony” at the school.

2GB reported Mr Griffiths' replacement, Robert Patruno, was allegedly threatened by two Middle Eastern men on Monday who told him: “We’re going to get you. We’re going to f--- you up. You dog.”

Mr Griffiths, who recently converted to Islam, is under fire for allegedly planning to exclude female staff from official events and claims he planned to allow only Muslim students into the school, according to News Corp .

Mark Scott, secretary of the NSW Department of Education, told 2GB radio this morning he was aware of the threats made against Mr Patruno, the former principal of Reiby Juvenile Justice Centre.

Former principal Chris Griffiths (L) was removed from the job. (Punchbowl Boys High School)

“Clearly there’s been some upheaval at that school. The principal and deputy have moved on from that school which came as a surprise to the community, and some people were upset,” Mr Scott said.

“It’s appalling. There’s no two ways around it. It’s disturbing which is why we’ve encouraged the principal to brief the police on it, which he did.”

Mr Scott said Mr Patruno had his mind focused on getting on with the job despite the threats, and wanted to focus on “calming down the community”.

“I think it will calm down. We all know teenagers,” he said, but quickly added if police identified persons of interest, the department would cooperate.

“If police have evidence, and have identified people who are of concern to them, even if school students, we will fully cooperate with them.

“I think it is an overstatement that the only people who were concerned about the change of leadership was radicalised youth,” he said.

Punchbowl Boys' High School.