Hackney council in east London threatened legal action, or government intervention at its request, unless the governors of Kingsmead School co-operated with an investigation into allegations against Ms Brown.
Beyond the particular circumstances, the row exposes the confusion at the centre of the Government's policy of shifting power and accountability away from local education authorities to school governors. John Patten, the Secretary of State for Education, will almost certainly become caught up in the dispute.
Gus John, Hackney's director of education, recommended suspension after preliminary investigations led him to conclude there was prima facie evidence of gross misconduct. The dispute centres on Ms Brown's refusal to allow her pupils to see the ballet Romeo and Juliet on the grounds that it was 'blatantly heterosexual'.
Subsequent concerns about alleged irregularities in Ms Brown's promotion to the post of head arose when it was revealed that Nicki Thorogood, with Ms Brown lives, had been chair of the board of governors when her appointment was made.
Mr Patten will be torn between support for Hackney's stand against political correctness and its tendency to support governors against education authorities. Since Ms Brown, 36, appears to have the support of most parents at Kingsmead, the Government's commitment to 'parent power' will also be tested.
Parents say Ms Brown was wrong to ban the Romeo and Juliet trip but have accepted her apology. Their claim that she is a good teacher is supported by the school's removal from the Department for Education's 'at risk' list since she took over. Last summer, inspectors from Ofsted, the education watchdog, commended the school's 'very good leadership' and said the head provided a good model.
Richard Reiser, National Union of Teachers' representative, said that Ms Brown was a member of Hackney Gay and Lesbian Teachers Assocation. She was being unfairly singled out by a 'homophobic' press. Last night, John McCafferty, leader of the Labour-run Hackney council, said it would be reluctant to carry out its threats but would do so if the governors did not fall into line.
'It is now up to the governors to accept their responsibilities and take action over these issues in the best interests of the school. The council has given them a reasonable way forward and I hope that they will accept it.
Mr McCafferty claimed that government reforms which brought in Local Management of Schools meant the local education authority was now unable to carry out its responsibilities. Without suspension, a full investigation was impossible but Local Management of Schools gave governors the power to defy education authorities. That was the 'internal contradiction' within LMS.
Mr Patten was urged to intervene and order Ms Brown's suspension by Harry Greenway, Tory MP for Ealing North and a former headteacher. Mr John said the Secretary of State could send inspectors into the school without being invited by Hackney council.
The Department for Education said that Mr Patten was aware of the case and he had no plans to step in unless the matter was raised formally with him. Last night a move to force a debate at a full meeting of Hackney council failed, frustrating an expected plea from some councillors for the Government to intervene.