The Qualifications and Curriculum Authority (QCA) says it will not probe claims David Blunkett misused his then position as education secretary.
David Blunkett: Welcomed statement
It has been claimed Mr Blunkett put pressure on the QCA, via a civil servant, to check if his son was caught up in an exam marking fiasco in 1998.
Dr Ken Boston, QCA chief executive, said he had no experience of any ministers making personal inquiries.
A spokesman for Mr Blunkett welcomed the statement from the QCA.
Dr Boston said the QCA regulates the exam system in England, but does not have any direct involvement with students.
Exams are set by the three unitary awarding bodies - AQA, Edexcel and OCR - and any issues regarding individual candidates would have to have been dealt with by them, he said.
The computer problems arose at the OCR awarding body in 1998.
Dr Boston said: "QCA reported on these in an audit issued five years ago: Neither myself, or other members of the current QCA Executive were in post in 1998 and we have no recollection of any issues from seven years ago.
"In my experience no minister or secretary of state has ever made any personal approaches to the QCA and were it to happen, or were I to discover that it had happened, I would immediately declare so publicly.
"With regard to the events of seven years ago, I regard this matter as closed."
A spokesperson for Mr Blunkett said: "David Blunkett welcomes the clear statement that the QCA does not deal with individual students and their reinforcement of the statement issued by the former chief executive Nick Tate, which made it absolutely clear that the recent story was not true.
"Mr Blunkett's son was fully aware of which exam boards he was sitting, everyone was aware of the problems there were, and his grades were not affected.
"As far as David Blunkett is concerned the matter is now closed."