As the only Catholic school in the country refusing to return to Church control once the opted-out sector is abolished, his defiance is being interpreted as a wish to ditch its faith.
The fire has been fuelled by a charged letter from Catholic bishops warning that those schools choosing anything other than aided status would no longer be Catholic in September.
The letter had the desired effect of whipping the Catholic grant-maintained schools into line - except for St Francis Xavier's College. But Brother Francis said: "We don't share the fears that our Catholic character is in danger. Our parents and parent-governors strongly support the school's Catholicity, but also strongly support foundation status."
All the school's pupils are Catholic and Brother Francis believes the school's religious ethos cannot be in doubt.
Six old Xaverians are in seminaries preparing for the priesthood, 95 per cent of pupils were entered for GCSE RE, 120 sixth-formers are preparing for AS-level Christian theology and the A-level is enjoying a boom.
The school has a strong financial incentive for going for foundation status.
It is in the middle of a pound;7 million project to bring its lower school, currently three miles away, on to its attractive suburban 26-acre upper-school site.
The school has already been allocated pound;3m from Department for Education and Employment and as a foundation school would receive 100 per cent funding for the rest. However, if it became an aided school it would have to find more than pound;1m from its own funds as the archdiocese cannot finance the scheme.
The Most Rev Patrick Kelly, the Archbishop of Liverpool, has called on David Blunkett to support the Church and refuse the school foundation status, but Brother Francis says he is confident of the Education Secretary's support.
Brother Francis played a key role in the national administration of GM schools. He has been a board member of the Funding Agency for Schools for four years, a member of the GM schools advisory committee since 1989, founder and chairman of the Association of Catholic GM Headteachers and consultant to the Schools Standards and Framework legislation.
He believes that the Government is taking forward best practice from the GM experiment and feels neither fear nor remorse at defying the Catholic Church whose objections he deems unfounded.
St Francis Xavier's, an 11-18 boys comprehensive (with girls in the sixth form), was founded by the Jesuits in 1842 and in 1974 trusteeship was transferred to the Brothers of Christian Instruction, the order to which Brother Francis belongs.
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