A state funded Jewish faith school has been caught blacking out questions on science exam papers.

The Oxford, Cambridge and RSA Exam board (OCR) launched an investigation into exam malpractice at the Yesodey Hatorah Jewish Voluntary Aided girls' secondary school after the National Secular Society formally asked it to follow up unconfirmed reports that teachers had redacted questions in this year's GSCE science exam.

The precise questions that were blacked out has not been revealed by OCR, but earlier this year a Jewish education consultant warned that evolution in the new GCSE science curriculum could pose problems for strictly Orthodox schools.

The investigation confirmed pupils were left disadvantaged by being unable to access 3 marks out of 75 for a unit in a higher GCSE science exam, and 1 mark out of 75 for a unit on a lower paper.

Earlier this year, Rabbi Avraham Pinter, principal of Yesodey Hatorah, admitted "sometimes Charedi schools, if they find anything in the paper which could be offensive to parents, advise children to avoid that question".

A spokesperson for OCR said: "We have tried to respect the religious and cultural sensitivities of this community whilst protecting the integrity of our exams. That said, we do not consider obscuring aspects of question papers to be good exam practice. We are raising the matter with the Department for Education and Ofsted as well as our fellow Awarding Bodies, through the Joint Council for Qualifications. We are also in the process of agreeing safeguards with the centre to ensure good exam practice in the context of today's pluralistic society. Ofqual are also fully aware of our investigation and its outcome."

Yesodey Hatorah was founded in 1942 and operated as a private school until 2005 when it opted in to the state sector. It was launched as a state school with a high-profile visit from faith school enthusiast Tony Blair, then prime minister.

Girls attending Yesodey Hatorah are strongly discouraged from going to university. According to Rabbi Pinter: "Our experience, is that the better educated girls turn out to be the most successful mothers. For us, that's the most important role a woman plays."

Stephen Evans, National Secular Society campaigns manager, said: "Faith schools such as Yesodey Hatorah not only impede social cohesion by segregating children along religions and ethnic lines, they also fail to prepare pupils for life outside of a religious community and deny young people the opportunity to reach their full potential.

"In this case we have so called educators putting religious indoctrination before education – all at the taxpayers' expense.

"Pupils being denied the right to answer exam questions by teachers pushing their own religious agenda is shocking enough. However, the wall of silence surrounding this incident, and that it took the NSS to ensure this matter was properly investigated, reveals the extent to which not upsetting 'religious sensitivities' is now deemed more important than a young person's right to a rounded education.

"This is an extreme example of a common problem throughout our state education system: children's education being compromised by the influence of religious organisations. The time has come to draw a line under this faith schools experiment and separate the realms of religion and state education. Our schools should be about teaching young people how to think, rather than what to think."