Bennett Memorial Diocesan School in Tunbridge Wells, Kent, asked Gillian Shephard, the Education and Employment Secretary, to disregard its application for grant-maintained status following a dispute with ministers over its admissions policy.
But Mrs Shephard indicated she had to approve the application because parents voted for opting out of local authority control.
In a letter to Bennett parents this week, Rosalind Plumley, the chairman of governors, said they were satisfied the school has held on to enough of its admissions policy to ensure its character remains.
Bennett Memorial had objected to Government demands that the school scrap a long-standing arrangement under which parents accepting a place at the school committed themselves to comprehensive education by withdrawing their children from 11-plus selection elsewhere in Kent.
Mrs Plumley said that following 18 months of long and frustrating discussions with the Department for Education and Employment, it had been decided that governors would still retain the power to give preference to parents who declare that Bennett is their first choice of secondary school.
"We have fought hard for the principle of allowing a genuine wide-ability school to sit alongside grammar schools, in the belief that this provided parents with true choice for their children's education. It has become clear during this debate that where grammar schools exist, the present government will seek to protect them from real challenge," she said.
A spokeswoman for Kent County Council said the authority had backed the school's attempt to withdraw its application, and was saddened it would now become grant-maintained.
"I'm given to understand that this is the result of intense pressure from the Department for Education and Employment and the potential shortage of capital funding from the diocese," she said.