Peter Peacock has accused newspapers of gross misrepresentation of facts on class sizes in maths and English classes in S1 and S2.
Reports suggested the Education Minister was already failing to hit targets to cut class sizes but Mr Peacock has hit back by pointing out that the target of no more than 20 is set for 2007.
The partnership agreement in May between Labour and the Liberal Democrats spelt out the cuts and the need to increase the number of teachers. But this was not expected to "be achieved during the summer holidays", the minister protests.
Figures for September reveal that the average maths class size in S1 was 26 and 25 in S2. In English, it was 26 in both years.
Only 12 per cent of S1 and S2 pupils were taught in maths classes of 20 or fewer and 28 per cent were taught in classes of more than 30. In English, only 8 per cent in both years were taught in classes of fewer than 20 and 12 per cent were taught in classes of more than 30.
Lord James Douglas-Hamilton, the Conservatives' education spokesman, called on the Executive to scrap meaningless targets. "Too many of Scotland's public services are failing and centrally imposed targets are part of the problem, not the solution," Lord James said.
He adds: "The voice of the professional on the front line is subservient to the political will of the man in the ministry. We should trust headteachers, teachers and parents to cater for parent and pupil choices by setting priorities for their schools and deciding how best to allocate their resources."
Fiona Hyslop, the SNP's education spokeswoman, said that there had always been a question mark over the resources set aside to reduce class sizes.
Only pound;78 million had been allocated over the next three years.