The authority is pushing schools in the direction of opting-out by aiming at education cuts of pounds 2m in secondaries this year.
Meanwhile, the budgets of primary schools, which the council expects to continue to run, have been protected. It has set aside money to meet the expected costs of secondaries opting out. Only four Wiltshire schools have opted out so far.
The council's policy is the first public sign of a trend towards authorities concentrating their decreasing resources on the primary sector, a trend predicted by teachers' organisations and education officials.
'We do not expect to see many of the secondary schools left in two or three years,' Mr Chalke said.
Wiltshire education committee's decision to exempt primary schools from the cuts was taken after a review of local management of schools. Mr Chalke said that the 43 secondary schools in the county had reserves of pounds 6m between them and that primaries deserved more equal funding, particularly now that they had to implement the national curriculum.
He said: 'As an administration we support the Government's plans for education. We are not actively promoting opting out but we are assisting any school that applies for grant-maintained status. We believe in local power and decision-making.'
Wiltshire has to make savings of pounds 4m on its education budget. It blames the cuts on overspending due to an increase in those eligible for free school meals and more young people staying on at school or college after 16.
Keith Small, leader of the council's Labour group, said the authority was budgeting for 15 grant-maintained schools. 'Why should other schools remaining in the local authority have to suffer because of grant-maintained status? Once one school goes there is going to be an avalanche of ballots.'
Nigel Gilhespy, head of the Matravers secondary school in Westbury, said that there was a difference of hundreds of pounds in funding for pupils in lower secondary school classes and upper primary classes. This should be changed, he said, but not by reducing secondary budgets.