Qualifications changes, including the advent of work-related diplomas over the next 18 months, could be thrown into question by the loss of personnel vital to the system's smooth operation, it warns.
The Examination Officers' Association (EOA) said many of its 2,500 members were considering their futures after being asked to do their jobs for as little as pound;10,000 a year.
The exams officer role has been transformed in most schools since 2003, when the school workforce agreement stipulated that the job should be carried out by administrators rather than teachers.
The association said exams officers were losing out after being included in a general "support staff" category in pay bands that failed to reflect their responsibilities.
With exams so central to modern school life, the role can include managing a budget of more than pound;100,000. Staff are also responsible for making and tracking entries, running the exams, often managing exam invigilators, and advising teachers on entry requirements.
Local authorities have been adjusting the salaries of many employees in a bid to ensure its staff are paid equally for the same kind of work. But the EOA warns that with council budgets tight, many salaries are being reduced. It calculates that the pay of an average exam officer is about pound;14,000 per annum.
Andrew Harland, its chief executive, has had many complaints in recent weeks. One was from an exams officer who said she was about to quit to become a legal secretary after being downgraded to "the same grade as the school's caretaker".
A National Assessment Agency (NAA) spokesman said: "The NAA strongly encourages examinations officers to ensure that the scope of their role, especially any management duties, is fully reflected in their job description, which should then be individually assessed in any re-grading exercise."
I CAN GET BETTER MONEY ELSEWHERE
Linda van Bregt, a senior administration officer for examinations at Littlehampton Community School in West Sussex, is worried about pay. A single mother, she faces funding her son through university on a salary of pound;24,500. Already at the top of the pay scale, she cannot progress further and will receive a salary increase less than inflation this year.
Yet she manages a pound;136,000 budget, organises exams from Year 7 optional tests to A-levels all year round, and takes responsibility for a team of 30 invigilators.
"It's a very, very rewarding job, but people coming into it are shocked by the level of work involved," she said. "I am considering leaving because I can get better pay for a similar level of work doing something else."
Gill Bradford, examinations officer at Coombe Dean School in Plymouth, said she would have to leave the job and the school she loves within two years because of a pound;3,200 pay cut.
Her salary is being reduced from pound;18,000 to pound;14,800 after a re-evaluation of jobs across Plymouth City Council. But Ms Bradford said she had huge responsibilities - managing a pound;100,000 exams budget and recruiting and training 24 invigilators. She also holds a professional exams officer qualification.
"We have a huge impact on students' experiences and have dealings with around 80 per cent of them," she said. "I have worked damned hard to get where I am now but, on hearing of Plymouth City Council's decision, I wonder why I bothered."
The Examination Officers' Association has written to Ed Balls, the Secretary for Children, Schools and Families, and is awaiting a reply.