This follows the highly publicised scramble to recruit additional markers and glitches with the authority's new and complex computer system.
David Elliot, the SQA's director of awards, told The TES Scotland that staff were "actively pursuing" the missing assessment data. "We are nering completion of this process but it is not yet complete," Mr Elliot said.
"The information outstanding is very small. It could well be that it concerns pupils who have not completed the units or have failed them. But we want the final certificate to be as complete as possible. We don't like loose ends."
Pupils who are unhappy with their marks should first discuss matters with their school, Mr Elliot said. Ultimately, the SQA's appeals mechanism is always available for those candidates who want to take things further.