As the Government presses admissions tutors to take a broader social spectrum of candidates, some are giving lower offers to children from deprived backgrounds.
A Times Higher Education Supplement survey in June found that 10 per cent of admissions officers gave special consideration to local state schools.
The new study is being conducted jointly by the Headmasters' and Headmistresses' Conference and the Girls' Schools' Association and results will be announced later this year.
Geoff Lucas, HMC secretary, said: "We have had anecdotal examples where practice does not seem to be quite as fair, meritocratic and dispassionate as one might hope, or universities have not been as explicit about entry requirements as one would hope."
Bristol University has admitted giving lower A-level offers to children from poorer backgrounds if they show potential. But spokesman Barry Taylor said: "There is no bias against independent schools. There is an absolute bias in favour of academic potential."
Pupils at independent schools get results well above average. The Independent Schools Council, whose members educate the vast majority of fee-paying pupils, said only 1,194 scripts out of the 96,103 submitted by its schools - barely 1 per cent - failed. Nearly 40,000 scripts, or 41 per cent, were graded A, almost double the average of 20.7 per cent.
But Margaret Tulloch of the Campaign for State Education said research had shown students from private schools did less well at university. Warwick University academics reported the students were less likely to get a first or upper second.
Newspapers rushed to compile league tables of private school A-level performance. Among the top ten were Winchester, St Paul's boys, St Paul's girls and North London Collegiate for girls.
Eton finished outside the top 20 in several tables.