Protests taking place outside a school, where a teacher was suspended for showing pupils a caricature of the Prophet Mohammed, were “not right”, the Communities Secretary said.
Robert Jenrick also said suggestions that a teacher at Batley Grammar School was in hiding were “very disturbing”.
His comments came as protesters gathered outside the school in Batley, near Bradford, West Yorkshire, for a second day on Friday, with police also at the scene.
It follows claims a member of staff had shown students a cartoon, widely reported as taken from the French satirical newspaper Charlie Hebdo, deemed offensive to the Islamic faith during a religious studies lesson this week.
Mr Jenrick said children should be taught “contentious issues appropriately”.
“It must be right that a teacher can appropriately show images of the Prophet Mohammed,” he told the BBC.
“In a free society, we want religions to be taught to children and for children to be able to question and query them.”
Speaking to Sky News, Mr Jenrick said: “I was disturbed to see scenes of people protesting outside the school – that is not right.
“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.”
On Thursday, the school “unequivocally” apologised for showing “totally inappropriate” material to children, and said a member of staff was suspended pending an investigation.
A protester speaking “on behalf of the Muslim community” read out a statement outside of the school on Friday, in which he said: “The teachers have breached the position of trust and failed their duty of safeguarding, and this issue must be addressed as a matter of urgency.
“We do not accept that the school has taken this issue seriously, given that it’s taken them four days to merely suspend only one of the teachers involved.”
He called on the entire British Muslim community to review the materials being taught in their children’s schools.
One protester, whose children attend the school, and who only wanted to be identified as Mr Hussain, told the PA news agency: “What people are trying to convey here to the media, and to the British public at large, is we would not like any form of extremism, any extremist viewpoints, to be taught to children.”
He said the western world “is at a loss in understanding the reaction” from the Muslim community when the Prophet Mohammed is “insulted in any way, shape or form”.
He said: “A Muslim is required to stand up when Prophet Mohammed is insulted, and when all the prophets are insulted, including all the prophets of the Old Testament, including Jesus.”
Labour MP for Batley and Spen, Tracey Brabin, condemned those who “seek to fan the flames of this incident”, and welcomed the school’s apology.
“No teacher should be facing intimidation or threats, there is no excuse for that,” she said.
“The focus must be on the welfare and education of the children at this school.”
Mr Jenrick said the Department for Education is working with the school and local council as it investigates the incident.
“What I can say is there has to be an appropriate balance – we have to ensure there is free speech, that teachers can teach uninhibited but that has to be done in a respectful and tolerant way and that’s a balance to be struck by teaching professionals and the schools concerned,” Mr Jenrick said.
Baroness Warsi, former chairwoman of the Conservative party, said the incident has been “hijacked by extremists on both sides” to create a culture war.
Speaking to the Today programme, the peer said 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.”
Geoff Barton, general secretary of the Association of School and College Leaders, said the school should be allowed to investigate the matter “without a running commentary in the media, on social media, and outside the school gates”.
Baroness Kishwer Falkner, who chairs the Equality and Human Rights Commission, said: “Children’s education should not be disrupted by protests in what has already been a difficult year.
“The school is taking action and ought to be trusted to do so. A teacher’s identity being shared, making them fear for their safety, is simply unacceptable and could result in enforcement action from the police.
“Schools are places where children learn about ideas, values, difference and respect. This sometimes involves exposing them to contentious issues and different views and ideas. For schools to meet their legal duty to foster good relations between people from different groups, this should be done in a balanced, respectful and sensitive way.”
The DfE came under fire for amplifying divisions after it branded the protests “completely unacceptable”, and said they included “threats” and “intimidation”.
Mohammed Shafiq, chief executive of Manchester-based Ramadhan Foundation, 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.”