It comes nine years after the commission's Room for Learning report which called for urgent action to reduce surplus places.
But the commission appears to be taking a benign view. Alastair MacNish, its chairman and a former council chief executive, commented: "We are concerned about the low levels of school occupancy in several areas across Scotland. However, we acknowledge that some councils are actively attempting to resolve this problem and we look forward to seeing steady improvement in future years."
The commission's report on performance indicators for children's services in 2002-03, published yesterday (Thursday), shows that the number of primary schools in Scotland that are 60 per cent occupied or less actually increased in recent years - although that still represented just a third of the 2,246 primaries.
Five councils (Argyll and Bute, Glasgow, Inverclyde, Shetland and the Western Isles) reported that at least half their primary schools were only 60 per cent occupied or less. Half-empty schools in rural areas are not unexpected while Glasgow and Inverclyde are now beginning a shake-up to reduce the number of primaries.
Others also face problems: Dundee, East Ayrshire, Highland, Orkney, South Lanarkshire and West Dunbartonshire are running with at least 40 per cent of primary schools 60 per cent occupied or less.
The picture in the secondary sector is more positive from the Accounts Commission's point of view. Just over one in nine secondaries are 60 per cent full or less, which represents 45 schools that are under-utilised compared with 59 the previous year. But 14 of the 32 authorities report they have no schools in that category.
At the other end of the scale, a number of councils - principally Aberdeenshire, Perth and Kinross and Edinburgh - report considerable pressure on accommodation, with some schools 101 per cent or more occupied.
While there is considerable variation in surplus capacity in schools, the commission provides part of the explanation: councils have discretion how they measure occupancy levels.
Some count gyms as teaching rooms, others do not; non-teaching rooms are treated differently in different parts of the country; and surplus accommodation which is used by the community is sometimes regarded as not being for school use.
The commission also reports that half of Scotland's councils have met the target to have all P1-P3 classes with 30 pupils or fewer, set by ministers some six years ago. In 2002-03, there were 7,750 P1-P3 classes of which fewer than 1 per cent had more than 30 pupils - a considerable reduction on the 7.2 per cent over that limit in 1999-2000.
The average class size in primary schools last session was 24.2, ranging from 15.3 in the Western Isles to 26.9 in East Renfrewshire.
Another target which shows signs of improvement is the time it takes to complete assessments of pupils' special educational needs, down on average to 25 weeks compared with 28 weeks in the previous two years. The commission says that the reduction is "considerable".
No reason is given for the improvement, which may be the result of improved staffing, particularly in the psychological service, fewer complex cases or speedier release of information provided by other organisations.
But the picture is not positive in all parts of the country with Moray taking the longest to complete SEN assessments at 49 weeks, compared with 13 weeks in Angus and Clackmannanshire. Yet Angus and Moray have broadly similar caseloads, 39 assessments carried out in the former and 44 in the latter.
The least likely target to be met is that all young people should leave council care with at least a Standard grade in English and maths, and Mr MacNish admitted that this was particularly challenging. Only 36.4 per cent of 16 to 17-year-olds who ceased being "looked after" last year had reached that level.
There are even larger disparities across the country than usual, from a 100 per cent record in Orkney (involving five pupils) to 9 per cent in West Lothian (11 pupils).