State-school teenagers are losing out even though their A-level results are on average two grades better than the candidates who are admitted from the independent sector.

The analysis by the Higher Education Funding Council for England (Hefce) will fuel controversy over access to elite universities as they seek approval to increase tuition fees to £3,000 a year.

Based on A-level performance, it suggests that a “missing 3,000” students — equal to one in ten entrants —who should be at top universities are either discouraged from applying or underestimated.

Sir Peter Lampl, chairman of the Sutton Trust, which commissioned the survey, said: “There are 3,000 kids from state schools who ought to be in these universities whose places are being taken by kids from independent schools.”

The study examined the proportions admitted to the top 13 universities, based on A-level points. The institutions are: Birmingham, Bristol, Cambridge, Durham, Edinburgh, Imperial College, London, the London School of Economics, Nottingham, Oxford, St Andrews, University College London, Warwick and York.

Among students who gained 18 points, for example, 10 per cent of those from fee-paying schools entered the universities compared with 5 per cent from the state sector. In the points system an A grade is worth ten points, a B eight, a C six, a D four and an E two.

Nearly 60 per cent of independent school students with 28 A-level points, equivalent to two As and a B, entered the best universities, but fewer than 40 per cent of those who achieved the same standard at state schools did so.

“Up to now the media have highlighted cases of bright students from independent schools who have failed to gain places at our top universities. In fact the dice are loaded in favour of independent school candidates,” Sir Peter said. “The research shows that the real casualties are students from state schools with high grades at A level who have a clear three to four-point handicap at top universities.

“The main reasons are that many qualified state-school students don’t apply to our leading universities and that offers are made not on actual grades but predicted grades, which in many cases are not accurate.”

The report, to be published next month, found that 10,400 of the 29,800 students admitted to the best universities in 2001-02 were from independent schools. But only 7,400 would have been expected to get in based on the qualifications of students who applied.

While the proportions of state and independent students at the universities rose in line with their examination grades, Hefce concluded that “the proportion going to a top institution is higher for students from independent schools”. It added: “In general, students from state schools have the same proportion going to top institutions as students from independent schools with about four fewer points.”

The findings emerged as Oxford was named Britain’s top university for the third year running in the latest Times Good University Guide. Nine of the universities highlighted by the report are in the Times top ten.

Hefce’s analysis found that the pattern was reversed at the former polytechnics that became universities in 1992. They accepted much higher proportions of entrants from state schools than from the fee-paying sector with the same A-level results.

Sir Peter, who funds summer schools to encourage state students to apply to top universities, said the study underlined the importance of reforming admissions so that students applied for places after they received their results.

Teachers at independent schools were more confident than their state counterparts at predicting high grades and encouraging students to aim for the best universities.

“It is not that the universities are biased. They don’t really have the data when they make the decisions.”

The best universities also had to work harder to attract bright applicants from state schools. All of the top universities except Warwick and York were well below Hefce’s “benchmark” targets for admission of state students. “If the missing 3,000 got in then the universities would hit their benchmarks.”

Alan Johnson, the Minister for Higher Education, said the study showed why the Government believed it necessary to establish the Office for Fair Access (Offa) as part of the Higher Education Bill.

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