Eric Martinez, director of operations for the Scottish Qualifications Authority (SQA), will leave the organisation at the end of October.
It is understood that Mr Martinez, who took over in March 2013, is leaving his post after a disagreement over whether his particular skills were suited to the wide-ranging demands of the job.
It is a fresh blow to the SQA, which has already seen two other senior members of staff leave this year, both to jobs in England.
News of Mr Martinez's departure emerged just more than a week before this year's National, Higher and Advanced Higher exam results are posted out to more than 150,000 candidates.
As director of operations, Mr Martinez was responsible for the current round of certification, but the SQA stressed the decision was in no way linked to the results, which they said would be delivered on time.
Since Mr Martinez went on gardening leave two months ago, the SQA's chief executive Janet Brown has taken over responsibility for the bulk of his work.
The SQA is now considering the best way to replace Mr Martinez, with one option being the appointment of two additional members of staff to cover both operational management and the associated IT infrastructure.
A spokesman for the SQA said: "Eric Martinez, who has made a significant contribution to SQA operations, will be leaving us at the end of October. We wish him every success with his future career.
"The 2014 National qualifications diet has been successfully implemented and the delivery of the qualification results is on track. SQA has robust processes and procedures in place to ensure the successful delivery of qualifications, involving a wide range of experienced teams."
Despite the guarantee that this year's exam results will be delivered on time, the departure is an embarrassment for the SQA in a year when it has been subject to unprecedented scrutiny.
In March it was announced that the head of curriculum development, Roderic Gillespie, was working his notice. He moved on after securing a better post with an English exam body.
Lena Gray, who worked as head of policy at the government quango, also left her job after securing a post south of the Border.
The SQA has also been widely criticised by teaching unions for the way it has delivered new National exams, which replaced Standard Grade this year.
Union leaders have accused the SQA of "dumping" the new exams on schools without sufficient support and with a lack of clarity over the nature of internal assessments, which have become increasingly prevalent under the wider Curriculum for Excellence reforms.
The SQA has also been criticised for confusion over whether schools or councils will pay for new charges for exam appeals by pupils.
Mr Martinez's profile on the business networking website LinkedIn refers to him as "A highly experienced senior executive with a proven track record of successfully transforming operations for growth, designing and implementing strategic international service plans and partnerships and building cost-efficient, customer-centric teams delivering at the highest possible level."
His previous posts have included an eight-month stint as senior vice-president of broadband company Ubee Interactive, based in Amsterdam in the Netherlands and, prior to that, seven years as vice-president of European operations for Taiwanese computer networking company D-Link.
Before that he was European operations manager of international relocation company Interdean.
The LinkedIn page records his education at Monash University in Australia, the world-leading Massachusetts Institute of Technology, and the Universities of Salamanca and Cambridge.