Cynthia Hall, of Wycombe Abbey School, said moves to make the exams more relevant to students meant they were not tough enough for bright pupils.
The girls' boarding school in Buckinghamshire has topped a GCSE league table of private schools.
Some 99 per cent of the school's GCSE entries were awarded at least an A grade in this summer's exams, the 89 pupils notching up 734 A* grades between them.
Mrs Hall said she was delighted with the results, saying it had been a "particularly good year group", but she raised concerns about the rigour of current GCSE exams.
"I would say that maybe it's to do with trying to make GCSEs relevant and applied to students," she said.
"It's completely understandable, it's so they can relate subjects to every day life.
"The problem with that is it may make those subjects more accessible. But in our point of view of academic studies for university, it makes it less 'academic'.
"They have become more and more accessible to students, but they are not as academically challenging, in that sort of sense of the world 'academic'."
Mrs Hall said that two or three years ago, scientists were arguing that something needed to be done about the state of science education.
"They created more applied and accessible courses, but it doesn't suit pupils who are academically minded and enjoy the toughness and rigour and want to study true science, rather than discussions about how it is used in life," she said.
As an example, Mrs Hall said that students do not learn so much about chlorine as a chemical any more, and how it reacts, and instead discuss if it should be in water.
"You need to know a bit of science, but not that much."
Wycombe Abbey currently offers International GCSEs
(IGCSEs) in maths and science, and is planning to offer them in French, Spanish, German, geography and English language.
IGCSEs have long been favoured by many private schools who believe they are tougher than traditional GCSEs.
In June, Education Secretary Michael Gove announced that state schools would be able to teach the qualifications from this month, reversing a decision made by the previous Government.
According to today's tables, based on data supplied by the Independent Schools Council (ISC) almost a third (29.5 per cent) of private schools' GCSE entries were awarded an A* grade, with 60.2 per cent awarded an A* or A.
Girls may be naturally less inclined to study maths and physics at A-levels than boys, research suggested yesterday.
A study found an underlying gender bias in subjects preferred by male and female students.
Researchers at the Institute of Education in London questioned 10,355 students aged 14 and 15 at 113 secondary schools in England about their intention to study maths and physics after the age of 16. Three times as many boys "strongly agree" with the idea of taking physics compared with girls.
INDEPENDENT SCHOOLS GCSE RESULTS 2010 BY COUNTY
Schools are ranked by proportion of exam entries awarded A or A*.
Hymers College 69.59
Pocklington School 50.64
Hull Collegiate School 40.57
St Peter's School 76.56
Ampleforth College 60.37
The Mount School, York 58.00
Bootham School 54.95
Queen Mary's School 48.89
Ashville College 46.62
Scarborough College 34.14
Read School 24.18
Sheffield High School
Birkdale School 63.80
Hill House School 45.80
The Grammar School
at Leeds 73.26
Wakefield Girls' High
Queen Elizabeth Grammar School 68.38
Bradford Girls' Grammar School 60.78
Gateways School 57.21
Ackworth School 43.15
Silcoates School 43.09
Fulneck School 31.93
The Grammar School,
*Based on data provided by the Independent Schools Council. iGCSEs are included.