In A-level history and physics, experts said, the disparity between today's syllabuses was greater than any change in standards over the past 20 years.
But each subject had easy and difficult syllabuses and grade As given by some boards would not have been given by others, said the inquiry report, published by the Government's Qualifications and Curriculum Authority.
Experts compared syllabuses, question papers, mark schemes, exam scripts and examiners' reports between 1976 and 1996.
At GCSE they looked at French, religious education, PE and geography. At A-level they examined physics, history, government and politics and German.
The history panel concluded: "Differences in grading standards between the awarding bodies in any one year were more marked than changes across time. While this is reassuring as to the maintenance of standards over time, it raises questions about the comparability of grades in any one year."
History examiners and academics said candidates graded A by the Oxford and Cambridge exam board showed less knowledge than Edexcel's top candidates.
In physics, Edexcel and WJEC candidates' exam answers were not as good as those given the same grade by other boards. The most demanding exam was also marked more severely while the easiest exam was very lenient at grade A, said the report.
In the 1996 government and politics A-level, Edexcel and WJEC A-graded candidates would not have got such a grade under any other board, a team of experts found.
The Government has already reduced the number of awarding bodies from five to three in an attempt to tackle disparities.
Today's exams are just as testing as 20 years ago, the report said, but are very different.
Exams now emphasise applying skills more than learning facts, and some subjects have changed focus. Physical geography has been scaled down in relation to human and social issues.
"GCE A-level Standards: A Review" and "Five-yearly Review of A-level Standards in 16-plus Examinations" are on the QCA Website, http:www.qca.org.uk.standards