Over the next few weeks, thousands of pupils across Scotland will sit the first National exams, which replace the old Standard Grades, but they will do so in an atmosphere of continuing uncertainty around the implementation of the Curriculum for Excellence (CfE).

Even before the curriculum was launched in 2010, many teachers questioned how prepared they were for the reforms and in the years since, concerns about the content of some of the courses and the size of teachers' workload have persisted.

Today the focus of concern has shifted to the cost of implementing CfE, with the Scottish Qualifications Authority (SQA), which developed the exams, recording a deficit of £3 million for 2013/14 and predicting a similar deficit for 2014/15. It means the Scottish Government has had to cover the spending gap by sanctioning an additional £2m grant to cover the SQA's cash deficit for 2013/14.

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Alan McKenzie, the acting general secretary of the Scottish Secondary Teachers Association, says the SQA should have been able to predict its expenditure and certainly the announcement of the deficit is unlikely to strengthen confidence in CfE.

However, a change on the scale of CfE was always likely to bring up unpredicted costs and, as the Scottish Government says, the deficit reflected some of the uncertainty over the likely costs of the curriculum. It is also not the first time the Government has had to offer additional funding to ensure the progress of the reforms.

Now the financial gap has been filled, the priority must be to ensure the SQA is properly funded and to ensure the rising costs of CfE do not affect pupils or schools as they try to make the curriculum work.

The central idea of the reforms is still sound: that the education system should be more than just a machine that churns out pupils capable of passing exams. Instead, it should foster broad-based learning likely to help pupils in the world they have to navigate after school. It is a principle that has won support in the teaching sector, including from the Educational Institute of Scotland (EIS).

But concerns about the implementation of the idea raised by the EIS and others have not gone away. Some teachers are saying they have not had enough time to adapt to the changes. There is also some confusion about the content of courses even though pupils are beginning to sit the exams this week.

Delay is obviously not now an option which means the SQA and teachers have to carry on and ensure the exams are the best they can be. The SQA also has to offer as much additional support as possible, particularly next year when the new Highers are introduced. As for the cost of that support, it must be closely monitored and controlled to ensure that it is not the schools, and ultimately pupils, who ultimately pay the price.