Amanda Spielman said leadership was “lacking” and there was no swift condemnation from the government during the row over teaching primary school children that same-sex families exist.
The Ofsted chief warned that “anxiety and concern” remain in communities ahead of relationships lessons becoming compulsory in all primary schools across England from September.
Speaking at the launch of the organisation’s annual report, Ms Spielman said she was “disappointed” that too often people are not willing to speak out openly about difficult subjects and concerns can be sidelined.
Government guidance, which says primary schools are “encouraged” to cover LGBT+ content if they consider it “age appropriate”, has been criticised for leaving teachers exposed.
Ms Spielman said it was “intolerable” that children and teachers were forced to walk into school past “placard-waving protesters” and listen to “diatribe blasting through megaphones”.
She added: “And yet there was no swift condemnation from the government and remarkably little from other local and national political leaders.
“The powerful voices that should have supported the children and the school were largely muted. Headteachers spoke of being isolated. Where leadership was desperately needed, it was lacking.”
Parkfield Community School, where protests began a year ago, brought back an amended version of the No Outsiders programme – which uses story books to teach children about same-sex couples – in order to address concerns.
Andrew Moffat, the assistant head at Parkfield Community School, told Radio 4’s Today programme that two books parents had issues with have been replaced following the protests.
Hazel Pulley, the chief executive of the Excelsior academy chain that operates the school, has called on the government to speak out more openly about the importance of integration in primary schools.
Ms Spielman said Ofsted was not afraid to speak out against the protesters and added that it has repeatedly shone a spotlight on difficult issues such as religious freedom and pupils’ rights.
Speaking on Tuesday, Ms Spielman criticised schools that illegally segregate pupils and give girls a worse deal than boys. She added that Ofsted has found teaching materials that censor women out of history, including Queen Elizabeth I, and books that say that a wife cannot deny her husband.
“Over and over again, we have reported findings that should have led to proper public discussion of some very difficult issues, only to see that few people are willing to tread in these sensitive areas and that real concerns drop out of sight almost at once,” she added.
Launching the report, the Ofsted chief hit back at criticism from heads over inspections and warned that schools are gaming the system to boost exam results, rather than serving the best interests of pupils.
Ofsted’s new inspection regime, introduced in September and focusing more on the quality of education on offer rather than exam results, has come under fire from school bosses.
An award-winning headteacher resigned last week after Ofsted inspectors graded the school as “requires improvement” due to concerns about “restricted” learning, despite an improvement in GCSE results.
The government is introducing compulsory relationships education for primary schools and compulsory relationships and sex education (RSE) for secondary schools from September.
In November, David Isaac, the chair of the Equality and Human Rights Commission, said primary schools should be free to teach children about LGBT+ relationships without consulting parents, as this requirement can create more anxiety and negativity.
Responding to the Ofsted annual report, a Department for Education spokesperson said they were “not complacent”.
“One of the key functions of a good regulator is that it highlights areas of concern and we will work with Ofsted, schools, local authorities and others to address the issues this report identifies,” the spokesperson added.