The Scottish Qualifications Authority has admitted it has some 13,000 incomplete course entries for students nine weeks before candidates are due to be sent examination results.
But SQA senior managers have assured the Scottish Parliament's education committee that checking information gaps is manageable.
Billy MacIntyre, SQA awards director, told the committee that the missing entries could, for example, refer to pupils who had left at Christmas and not been removed from the system or those who had changed courses.
A total of 140,000 candidates were sitting exams this year, involving 250,000 course entries.
Bill Morton, SQA chief executive, said: "We always knew there were some results we would receive in June so it shouldn't be a cause for concern or alarm."
Thousands of Scottish candidates were hit last year by the fiasco of missing or inaccurate exam results.