The government was "too slow to respond" to "mob" protests over LGBT teaching outside Birmingham schools, according to the woman tasked with challenging extremism.
Sara Khan told the BBC's Panorama more support should have been given to head teachers dealing with demonstrations.
Ms Khan was appointed by the home secretary to lead the Commission for Countering Extremism.
She said the Department for Education "could have done so much more".
"I think they were too slow to respond. There's a lot of confusion about what's actually being taught and I think the DfE could have played a very important role in clarifying to parents this is what's actually being taught, not the misinformation that we're seeing out there," said Ms Khan.
Protests began at Parkfield Community School, where most pupils are Muslim, in February. Parents called for an end to the use of story books featuring same sex couples, as part of a programme teaching about equality.
Protesters chanted "Our children, our choice", arguing their religion did not accept homosexuality.
Weeks later, the school suspended its "No Outsiders" programme, to consult with parents.
