New figures have revealed a “troubling” difference in subject attainment between independent and state school pupils – with fee-paying pupils strongly outperforming their counterparts in history and geography, but only slightly in science.

A report by Durham University and the Centre for Evaluation and Monitoring, commissioned by the Independent Schools Council, shows independent school pupils outperformed their state school counterparts by an average of 0.77 of a grade in history, by 0.72 of a grade in French and 0.62 of a grade in geography in 2014.

At the other end of the scale, pupils at independent schools performed just 0.22 of a grade better in chemistry and 0.35 of a grade better in both biology and physics.

The data has been described as “troubling” by Rebecca Sullivan, chief executive of the Historical Association, while Association for Science Education chief executive Shaun Reason called for further investigation into the reasons behind the difference between subjects.

Ms Sullivan said there were “many excellent teachers of history in state schools”, but pointed to research which showed independent school pupils were more likely to study history as a standalone subject and learn from a subject specialist.

The research, by former history teacher and University of Oxford academic Katharine Burn, revealed 97 per cent of independent schools taught history as a standalone subject to year sevens, compared to 82 per cent of state schools.

It also found that pupils learned from subject specialists rather than those with broader humanities knowledge in 79 per cent of independent schools, compared to 41 per cent of state schools.

Mr Reason said the findings were “very interesting”, and questioned whether the disparity might be down to the fact individual sciences tended to be taken by more able students in state schools and that double science had not been taken into account.

He added: “I would like to think that it was partially as a result of the hugely supportive science community that works closely together to offer teachers and science technicians professional development and support and sponsored school-based initiatives.”

The Independent Schools Council (ISC) has said that one of the report’s main findings, that independent school pupils benefited from “the equivalent of two additional years of schooling by the age of 16”, was proof of that they were “worth paying for”.

But general secretary Julie Robinson said the ISC was “acutely aware” of the difficulty in comparing different systems of schooling and drawing accurate conclusions, and that there was “much excellence to be seen in schools of all types”.

The ISC-commissioned research can be found online here, and the Historical Association’s research is available here.