The government put "extreme pressure" on a school to stop lessons on LGBT relationships, a chief executive said.
Hazel Pulley said Parkfield Community School suspended the teachings following "frantic phone calls" from the Department for Education (DfE).
"The DfE really wanted the protests to stop. They wanted it out of the press," said Ms Pulley, who is head of the trust which runs the school.
The DfE is "working intensively with the school and parents", it said.
Ms Pulley also urged new Prime Minister Boris Johnson to step in and make guidance on the issue for head teachers clearer or risk further divisions in communities.
Parkfield's No Outsiders equality programme, which encourages children to accept differences in religions, families and relationships, was suspended in March amid angry protests at the school gates.
Protesters stated the subject matter contradicted the Islamic faith and that primary-age children were too young to be aware of same-sex relationships.
As tempers flared, Ms Pulley said she felt "extreme isolation" and was "totally on my own to deal with something that was coming at us with great force".
"We suspended the programme because we came under extreme pressure from the DfE," she told the BBC.
"It occurred on a Wednesday evening before the next protest that was planned for the Thursday morning.
"They wanted the protest to stop and I understand that but the school was doing nothing wrong.
"I don't think this had ever happened in schools in our country before where parents would stand outside a school and really shout using megaphones and keep children out.
"It worried me because I felt that it was empowering parents to realise that if you shout and scream outside a school or [there's] something you don't agree with, you can stop it, but it also made it look like the school was doing something wrong, which it wasn't."
The BBC has seen a letter to Birmingham MP Jess Phillips in which Schools Minister Nick Gibb states: "I am clear that at no point did officials from the department pressure the school into pausing or stopping the No Outsiders programme."
The Department for Education said in a statement: "Any suggestion that the dispute should be kept out of the media was absolutely not an attempt to silence the school, but a bid to bring an end to protests, encourage consultation and ensure tensions weren't further inflamed by sensationalist coverage."
No Outsiders, which includes books about two male penguins that raise a chick together and a boy who likes to dress up like a mermaid, will be resurrected at the school in September.
Ms Pulley urged Mr Johnson to intervene in the continuing row, saying DfE guidance on how to teach equality issues was "too grey".
"Saying that the teaching or raising awareness of LGBT people is up to head teacher's autonomy is not acceptable," she said.
"If we don't get this sorted now this is going to grow and community cohesion will become more of a challenge - it's just going to get worse," Ms Pulley added.