Principal of the east London's St Stephen's School, Neena Lall had last month decided to impose a the ban on girls under eight on the grounds that Islamic teaching did not require girls to wear it until reaching puberty.
But she was forced to reverse decision after a social media campaign, which included her being likened to German dictator Adolf Hitler.
Speaking in favour of Lall, chief of the Office for Standards in Education, Children's Services and Skills (Ofsted), Amanda Spielman warned that religious extremists were "perverting" education.
Ofsted is a non-ministerial department of the UK government, reporting to Parliament.
"I want to be absolutely clear, Ofsted will always back heads who take tough decisions in the interests of their pupils,"Spielman said in a speech to a Church of England schools conference.
"School leaders must have the right to set school uniform policies in a way that they see fit, in order to promote cohesion," she added.
Spielman said it is a matter of "deep regret" that the school, considered one of the best in the UK, has been subjected to "a campaign of abuse by some elements within the community".
"Rather than adopting a passive liberalism, that says 'anything goes' for fear of causing offence, school leaders should be promoting a muscular liberalism...schools must not be afraid to call out practices, whatever their justification, that limit young people's experiences and learning," she noted.
Spielman's message to schools in Britain is that they have a responsibility to "tackle those who actively undermine fundamental British values or equalities law".
School leaders may need to make "uncomfortable decisions" in the interests of their pupils, and not assume that the most conservative sections of a particular faith represent all its members.
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