The Scottish Qualifications Authority (SQA) was reacting to news Roddy Gillespie, the body's head of Curriculum for Excellence (CfE), was taking up a post with another exams body.
The Scottish Labour Party suggested Mr Gillespie was the "main architect of the exams" and warned he was "clearing off before they are sat, marked and reviewed".
However, the SQA said Mr Gillespie was one of many officials delivering the new National 4 and National 5 exams, which begin in the last week of April and run until June 6. His role has been to develop exams rather than deliver them.
"Roddy has built a strong team which will continue to work as part of that extensive directorate group to develop and deliver the new CfE qualifications, and we will be working with him over the course of his 12-week notice period to ensure a smooth handover," an SQA spokesman said.
Kezia Dugdale, Labour's education spokeswoman, will raise the issue at the Scottish Parliament today in questions to Education Secretary Michael Russell.
However, a Scottish Government spokeswoman stressed the new qualifications would be unaffected by the change in personnel.
"The individual is one of a team of people who have been involved in leading the SQA's activity in developing the new exams and he remains in post until after the current exams, by which time all development work relating to the new Highers will be complete," she said.