Bridget Phillipson has called for a “thorough and robust” inquiry into the trust running a school which cancelled a visit from a Jewish MP.
The education secretary told Cabot Learning Federation that it would have to begin a targeted investigation.
If the result is deemed not up to standard, it could lead to an improvement notice being issued by her department to the federation.
The inquiry will run alongside the Ofsted inspection of Bristol Brunel Academy, which began on Thursday.
The school’s watchdog said it was looking into claims the school “may have been intimidated into cancelling a visit” by Damien Egan.
Ms Phillipson told The Times: “I have already made my views clear… what happened to Damien Egan is completely unacceptable, and I am determined to get to the bottom of how it occurred.
“That is why I have asked Cabot Learning Federation to commission an independent investigation examining the processes and culture that allowed this to happen. Alongside Ofsted’s inspection of the school, this investigation must be thorough and robust.
“Learning lessons from this case is not optional – it is essential. If failings are identified, I will not hesitate to take further action.”

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Mr Egan, who is vice-chairman of the Labour Friends of Israel group, was scheduled to visit the academy in September, but the visit was cancelled due to protests from pro-Palestinian activists planned for that day.
Teachers threatened to wear keffiyehs to school, with the visit needing to be postponed due to safety concerns.
Among those mounting a campaign against his attendance were left-wing members of the National Education Union.
They cited what they termed “safeguarding concerns” and highlighted the MP’s role as vice chair of Labour Friends of Israel.

Those behind the campaign claimed to speak for teachers, parents and local residents, pointing to Mr Egan’s connections to the pro-Israel parliamentary group as justification for blocking his visit.
Communities Secretary Steve Reed disclosed the incident while addressing the Jewish Labour Movement’s annual conference.
“I have a colleague who is Jewish, who has been banned from visiting a school and refused permission to visit a school in his own constituency, in case his presence inflames the teachers,” Mr Reed revealed.
“That is an absolute outrage,” he concluded.

When asked how the Government would respond, the minister made clear there would be consequences.
“They will be called in, and they will be held to account for doing that, because you cannot have people with those kinds of attitudes teaching our children. You just can’t have it,” Mr Reed told Jewish News.
A source at the Department for Education (DfE) said the purpose of the trust’s inquiry would focus on two points.
It would hone in on what happened leading up to the event and to detail the culture of the trust.
The second point would be working with them to determine the terms of reference and appoint an independent investigator.
The DfE can issue notices to improve academies in several aspects, but does not hold the power on educational grounds.
It can share notices on financial management or governance grounds, but these are very rare, with only seven disclosed last year.
The Cabot Learning Federation said: “We have agreed with the Department for Education to commission an independent review. We look forward to engaging fully with this process.
“This follows a highly constructive two-day visit from Ofsted; we thank the inspection team for their professionalism, and we look forward to seeing the outcome in due course.
“The promotion of inclusion and rejection of discrimination has long been enshrined in the CLF’s core values. We take our duties to safeguard and protect our community, to comply with the Equality Act, and to educate young people about British values and their role in society extremely seriously.”
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