As pupils throughout Scotland started their exams, two of the organisations' senior figures told The TES Scotland, in an exclusive interview, that the technology critical to the delivery of this year's exams is "going to work the way we require".
But, according to a report to the Scottish Parliament's education committee from the three unions which represent half of the SQA's 600 staff, information technology "is still inadequate to meet the needs of the task confronting us".
The system is fragmented with information being handled by disparate groups, increasing the chances of data going missing and mistakes being made, the unions claim.
Unison, the MSF and the TGWU added in their evidence to the MSPs that there is still "a certain uneasiness about data and our ability to handle it". The decision to deal with school-assessed unit results in the same way as last year has given rise to fears that the SQA would be swamped when these are submitted during May.
But Colin Urie and Billy MacIntyre of the SQA say the volume of results will be more or less the same as the volume of entries and the entries have all been dealt with.
Some 300,000 entries have already been processed out of almost a million. "We will get a peak but we have the capacity to deal with it," Mr MacIntyre, the authority's head of data management and interim director of awards, says.
Colin Urie, head of the information technology unit, said it was "absolutely not true that the SQA is three months behind schedule. "Everything we have received we have processed," he said. "If you process it, it's in the system and you don't need to worry about it. If you process it and there is a problem, you have time to fix it."
Mr Urie also treated with derision repeated reports of alleged problems between computer systems in schools and the SQA. Mr MacIntyre revealed early thinking on piloting a web-based sytem which would give every school and college immediate access to the SQA.
The unions' major complaint is being excluded from decisions by management. They say poor communications are driving stress up to "a worrying level".
The unions were particularly annoyed by the appointment of general managers who have reportedly been promised a pound;10,000 performance bonus on top of their pound;50,000 salaries if this year's exams are delivered successfully.
"If that is indeed achieved, it will be due to the collective efforts of all the staff, not just half a dozen senior managers," Gordon Rogers, senior MSF representative in the SQA, told the parliamentary committee.
The unions went on to say, however, that management had improved its attitude recently, although Gordon Casey, regional officer with MSF, dated this from the moment it heard the unions were to give evidence to the committee. Three staff representatives have been invited to sit on working groups. A briefing letter went out to all staff last weekend.
Mr Casey told the MSPs: "I would encourage you to keep up your dialogue with the SQA so it will keep up its dialogue with us."
ScotlandPlus, page 4