On one maths paper, only 22.5 per cent was required to attain a C grade, while 32 per cent was sufficient on a physics exam.
For two history papers, pupils could gain A*s with 61 per cent, although they also needed to score more than 90 per cent on their coursework to achieve the top grade.
Professor Alan Smithers, of Buckingham University, said: "To award a C grade on 32 per cent in physics and 22.5 per cent on a maths paper really is very low and gives a misleading impression. It may be saying to the candidates that they are better at this subject than they really are."
On Wednesday, the Association for Science Education expressed concern after the Joint Council for Qualifications recommended that the proportion of easier questions in foundation science GCSE papers should rise from 55 to 70 per cent.
AQA's conventional biology, chemistry and physics GCSEs are all assessed through a combination of coursework and exam papers.
For physics, 32 per cent was needed to achieve a C in the exam; for chemistry, it was 38 per cent; for biology, 39 per cent. In all three, pupils also needed to score a minimum of 63 per cent on coursework for a C grade.
An AQA spokeswoman said grade boundaries were set in accordance with the Qualifications and Curriculum Authority's code of practice.