Parents voted by 79 to 46 against opting out. Almost 72 per cent of the school's 174 parents took part.
The ballot was prompted by an acrimonious row over plans to merge the Isles of Scilly Secondary School with some 113 pupils with 110 pupil-strong Carn Gwarval Primary last year.
The decision still rests with Gillian Shephard, Education and Employment Secretary .
Last winter the population of around 2,000 on the islands 30 miles off the coast of Cornwall was divided about the merger. Secondary school governors, some councillors and parents accused the education authority of exceeding its powers and of a hidden agenda to shake up the school's management, a charge strongly denied by the council Although governors decided not to hold a ballot, the required number petitioned to hold one in March. A member of the Grant Maintained Schools Foundation was invited to address a meeting. Shortly afterwards the council invited parents to an open meeting in the town hall which was addressed by Martin Rogers from the rival organisation, the Local Schools Information Unit.
The merger was recommended by Duncan Graham, former head of the National Curriculum Council, who was appointed last summer as an independent expert by the council to look at options to solve funding problems triggered by falling rolls and the consequent reduction in Government grant.
He reckoned that around Pounds 87,000 needed to be saved of which Pounds 61,000 could come from the merger as a senior management layer could be lost. Governors of the secondary school contested Professor Graham's statistics and issued statutory objections to the merger.
Michael Hicks, the current chairman of the council, said that he was delighted with the decisive result.
A Department for Education and Employment spokeswoman said that Mrs Shephard was still considering her decision but, in any case, a successful opt-out vote would not have affected the outcome.