Islamic students at a Sydney public school threatened to behead non-Muslim staff and declared themselves ISIS sympathisers, staff alleged.

Police feared students at Punchbowl Boys High School were being radicalised after principal Chris Griffiths did not cooperate with a de-radicalisation program.

Mr Griffiths and deputy principal Joumana Dennaoiu were removed from their roles at the Muslim-majority school after an investigation by the Education Department.

Punchbowl Boys High School Principal Chris Griffiths (pictured) was stood down on Thursday

The pair were stood down for allegedly stopping female teachers from participating in official events such as the Year 12 graduation ceremony, along with other issues.

Several employees claimed non-Muslim staff were verbally attacked, including with threats of beheading, by Muslim students declaring themselves ISIS sympathisers, according to The Australian.

There was no suggestion either of the pair condoned the threats, but the incidents were not reported to police.

The 'actively hostile' relations were so bad police liaison officers couldn't access the government school for the past 2.5 years.

Officers said Mr Griffiths converted to Islam in 2014 and claimed relations between police and the school broke down after he was appointed two years ago.

Islamic students allegedly threatened to behead non-Muslim staff and claimed to be ISIS sympathisers, staff claimed

'Students were being told that if "the pigs" stop you, to film them and refuse their directions,' a senior constable told the Daily Telegraph.

'The students were being led down a dangerous path by the principal. We had concerns about radicalisation,' they said.

The Education Department said it conducted an 'extensive appraisal of the school’s policies, procedures and management', prompted by a series of serious staff complaints in 2016, before removing the pair.

It said the investigation revealed 'a high level of staff disunity and disharmony' and 'increased disengagement' of the school from the community.

'The former principal and deputy principal are still employed by the department but are currently on leave and will not return to the school,' it said.

The pair were stood down for stopping women teachers from participating in official events such as the Year 12 graduation ceremony, along with other issues

Mr Griffith's predecessor Jihad Dib, who is now the NSW state MP for Lakemba, said exclusion of any kind was wrong as public schools were there for everyone.

Under Mr Dib's leadership, the school was transformed from a campus controlled by Middle Eastern gangs where violence and drug dealing were rife, to a high performer with much better literacy and numeracy rates.

The Department told Daily Mail Australia new principal Robert Patruno, who previously ran the education unit inside Reiby Juvenile Justice Centre, and a deputy principal started work on Friday.

'Importantly there is no disruption to teaching and learning and the education opportunities provided to students,' it said.