Reports suggested that Mr Fraser, aged 51, had clashed with ministers but both parties said that while discussions had been "robust", this was not a factor in his departure.
The SQA is sticking to the party line that Mr Fraser is opting out for personal reasons after being in post for around 20 months. He has gone on holiday and is not expected to return before he finally quits at the end of October.
Anton Colella, aged 42, director of qualifications, will be acting head until a successor is appointed and will be well placed to take over a fast-revolving seat. Ron Tuck and Bill Morton have vacated the position in the past three years.
Mr Colella comes from a schools background and has been the public face of the organisation while the chief executive has reorganised internal structures.
Mr Fraser has spent most of his working life in health-related administration and is a former chief executive of Dumfries and Galloway Primary Care NHS Trust. He has never been a comfortable frontman for the highly technical examinations industry.
Lack of short and long-term funds is said to be the source of a bust-up with the Executive but this has been strenuously denied. The Executive has put in pound;17 million this year plus another pound;1.42 million to meet rising costs.
The authority had argued for a 10 per cent rise in exam fees over the past year but ministers cut this to 5 per cent. It has also spent more than anticipated on subject reviews. The problems are blamed on the rising costs of Higher Still with more students taking more subjects at more levels.
Some teachers claim reforms to the still contentious English Higher were down to cost-saving.
An Executive spokesman commented: "Far from falling out, we are working closely with the SQA to move towards a three-year funding model to deliver value for money."
Inside the SQA it is alleged many were unhappy with Mr Fraser's management style after he dispatched a tier of 29 unit or middle managers who were familiar with the details of the exam bureaucracy. Relationships at senior level were said to be strained.
As ever in sudden departures, the SQA and the Executive thanked Mr Fraser for his contribution in ensuring another year of successful National Qualification results. When he took over the post his target was a three-year spell at the top. Now that he has opted out halfway through, he will be given credit for keeping the SQA ship a low profile.
Until this week.