The row over reports that a cartoon of the prophet Muhammad was shown to pupils at a West Yorkshire school has been “hijacked by extremists on both sides”, according to a former Conservative party chair.

Sayeeda Warsi told BBC Radio 4’s Today programme she had spoken to pupils and parents over the past 24 hours and “it’s obvious that many pupils were left distressed because of what happened”.

She said: “What we’re forgetting in all of this is the most important party in all of this, which is the kids and their learning.”

Dozens of protesters gathered outside Batley grammar school near Bradford on Thursday after claims that a member of staff had shown students a cartoon deemed offensive to the Islamic faith during a religious studies lesson. More protesters gathered outside the school for a second day on Friday, with police also at the scene.

The school “unequivocally” apologised for showing “totally inappropriate” material to children and said a member of staff had been suspended pending an investigation. But the Department for Education branded the protests “completely unacceptable”, and said they included threats and intimidation.

The department’s response was criticised by the Manchester-based Ramadhan Foundation. Mohammed Shafiq, the chief executive of the organisation, said the community rejected any violence or threat of violence and the incident “will now be hijacked by those who have an interest in perpetuating an image of Muslims”.

The communities secretary, Robert Jenrick, told Sky News on Friday he was “disturbed to see scenes of people protesting outside the school – that is not right”.

He added: “We shouldn’t have teachers, members of staff of schools, feeling intimidated, and the reports that a teacher may even be in hiding is very disturbing. That is not a road we want to go down in this country, so I would strongly urge people who are concerned about this issue not to do that.”

Earlier, Shafiq had said: “It is alarming that the Department for Education chose to amplify those divisions by attacking the parents and pupils rather than looking how we can come together to have a respectful discussion and seek an end to this issue.

“There is still time for calmer heads amongst the department and we urge them to seek language that brings us together and address the issue without deflecting. The education sector has a duty to protect the needs of all pupils and we are heartened that the school leaders recognise the pain and suffering caused by this incident.”

West Yorkshire police previously said they were called to the protest at about 7.30am on Thursday. A spokesperson said the school road was closed for a short time, no arrests were made and no fines were issued.

In a statement, the school’s headteacher, Gary Kibble, said: “The school unequivocally apologises for using a totally inappropriate resource in a recent religious studies lesson. The member of staff has also given their most sincere apologies. We have immediately withdrawn teaching on this part of the course and we are reviewing how we go forward with the support of all the communities represented in our school.

“It is important for children to learn about faiths and beliefs, but this must be done in a sensitive way. The member of staff has been suspended pending an independent formal investigation.”