Two-year secondary schools are set to be wiped out in Scotland. This will be due, in part, to A Curriculum for Excellence - but the plans, by the Western Isles Council, have already fallen foul of opposition from education ministers and parents. They could be an early test of the Government’s opposition to rural school closures.

Although the Western Isles education committee decided to reprieve two of the schools on Tuesday, this was because of intervention by the clergy; they do not have seats on the full council, which is expected to overturn the decisions next week.

The Western Isles is the only authority in Scotland where P1-S2 schools are still in existence. But this rare breed, set up to retain young people in their communities for as long as possible, is facing extinction, because officials believe the schools are incompatible with the new 3-18 curriculum.

Murdo MacLeod, director of education in the Western Isles, insists it is vital that the 40-school estate is rationalised on curricular and cost grounds. And Morag Munro, chair of the education and children’s services committee, says dwindling rolls mean that the council’s expenditure on education, which totals pound;38 million, exceeds the Government’s grant by around pound;7 million.

The two S1-2 secondary departments in the schools enjoying what may be a temporary reprieve - Daliburgh in South Uist and Bayble in Lewis - are among seven 5-14 in the Western Isles.

This marks the beginning of a fraught series of consultations, scheduled to end in March next year. By June 2011, the council aims to close the remaining five two-year secondaries - Paible in North Uist, and Shawbost, Lionel and Back and Sgoil nan Loch (all Lewis).

Fiona Hyslop, the Education Secretary, and Maureen Watt, the Minister for Schools and Skills, have told the council that structural change is “emphatically not” a requirement of A Curriculum for Excellence. However, a spokeswoman for the Scottish Government denied this was an intervention.

Last year, Ms Hyslop said she wanted to introduce a “presumption against closure of rural schools” and the Government is on track, according to the spokeswoman, to consult publicly this spring on a new law. In the case of Daliburgh, Ms Hyslop will be set a test case for her policy since she will have the final say because of the 21-mile distance faced by pupils going to the next available school, at Lionacleit in Benbecula (the threshold triggering ministerial intervention in secondary closures is 10 miles).

Mr MacLeod points out that having two-year secondaries “flies in the face of arrangements which are virtually universal for delivery throughout Scotland”. He gives four main reasons for closing the schools. A Curriculum for Excellence tops the list, followed by the need to release and redirect resources, declining school rolls, and tighter financial settlements.

S1-2 schools cannot offer pupils the variety of subjects required under A Curriculum for Excellence, Mr MacLeod claims.

“The current structure in the P1-S2 schools is a good fit for the current 5-14 curriculum, but will not cater for delivery of the new curriculum as schools must be able to offer an S1-3 curriculum,” he says.

Cost was another factor. School rolls dictate the level of government funding and numbers are falling in the Western Isles. Last year, the number of children entering P1 was half that in P7. Daliburgh is one of the most expensive state secondaries in Scotland; in 2006-07 it cost almost pound;25,000 to educate each of its 15 secondary pupils against a Scottish average of pound;6,120.

Even though the roll has risen to 22 pupils this year, Mr MacLeod argues, keeping such schools open is draining resources to such an extent that basics, such as maintenance of buildings, are unaffordable.

Parents are “dead against” the closures, according to Donald MacLellan, chair of the Parent Teacher Association at Daliburgh. He says parents are unhappy with children in the early years of secondary having to travel for two hours every day. He also expresses concerns about the impact the move would have on the community: “We are trying to get young families back to the island, but they won’t come if there is no decent provision for education. Everything is becoming centralised.”