Britain's leading medical journal was threatened with legal action by the family doctors' professional body over a report that considered whether there was racial bias in the way that trainee GPs are examined.

The article by a leading academic in the British Medical Journal, (BMJ) said that "subjective bias owing to racial discrimination" could not be ruled out as a reason for consistently high failures rates among black and Asian trainees taking the Membership of the Royal College of General Practitioners (MRCGP) exam. Doctors must pass this to practise as a GP in the UK.

Before the report's publication, the Royal College of General Practitioners (RCGP) wrote to the journal, asking it to change both the title, which included the word "discrimination", and the summary of the paper, which contained the explosive warning over possible racial bias. The college followed up its request with a lawyer's letter saying it considered the report to be "defamatory".

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The revelation comes amid a furious row over the report, which the BMJ eventually published in full two weeks ago. Its author, Professor Aneez Esmail, a leading academic and GP, has accused the RCGP of "refusing to accept there is a problem" with the exam and trying to brush concerns about possible bias "under the carpet". The college is facing a judicial review brought by the British Association of Physicians of Indian Origin (Bapio) over low pass rates for doctors from ethnic minorities in the clinical skills assessment (CSA) component of the exam, which involves a mock GP consultation, with an actor posing as the patient.

Professor Esmail's report for the BMJ was published on the same day as an official review of the exam, also written by him, which was commissioned by the General Medical Council following long-standing concerns about its fairness. His six-month review found that ethnic minority doctors trained in the UK were four times more likely to fail the exam at the first attempt than UK-trained white candidates, while ethnic minority doctors trained abroad were 14 times more likely to fail. The two reports used the same data.

In the GMC report, Professor Esmail and co-author Professor Chris Roberts say they cannot "confidently exclude bias from the examiners in the way that they assess non-white candidates", but did not include the specific statement that "subjective bias owing to racial discrimination" cannot be ruled out – leading to disagreement over their conclusions.

The RCGP responded with dismay to the BMJ report. Dr Clare Gerada, chair of the RCGP, said the GMC report had found "no evidence of discrimination" and accused Professor Esmail of contradicting himself by "misleadingly" suggesting the RCGP may be biased in the way it assesses candidates. However, Professor Esmail told The Independent on Sunday that he "absolutely refutes" any notion that his report for the GMC exonerated the RCGP, and claimed the college was guilty of attempting to downplay his findings ahead of the Bapio judicial review.

"My report clearly stated that there were problems," he said. "It identified major differences in outcome between British-trained ethnic minority graduates and white graduates, and also showed big differences between international graduates and British graduates. I absolutely refute this notion that I exonerated them."

Bapio has gained permission to take the RCGP to judicial review over the exam. It is also seeking to include the GMC in the claim, but was denied permission, a decision which it is appealing at a hearing this week.

Fiona Godlee, editor-in-chief of the BMJ, confirmed that the journal had been asked by the RCGP to make changes ahead of publication. "We received emails from the college asking us to change the paper, to make changes to the title and the abstract of the paper and to reissue the press release," she said. "We responded saying that we had no plans to [do so]. This was followed by a lawyer's letter repeating the demand and adding that they considered it defamatory. We said that we felt it would be damaging to our reputation and theirs if we made a change to a research paper in response to their request."

Dr Ramesh Mehta, president of Bapio, said that his concerns over discrimination went beyond the exam, and that the medical establishment was guilty of institutional racism. "There is stereotyping of ethnic minority doctors, that they are not up to the mark," he said. "This is the effect of institutional racism, which is reflected into the examination scenario. There is no doubt that there is a problem. It is not the whole profession, but when it comes to the establishment, there is a problem."

Dr Gerada said: "The RCGP takes equality and diversity issues extremely seriously and strongly refutes any allegations that the MRCGP exam is discriminatory in any way. We already take comprehensive steps to ensure that the exam is fair and equitable to all candidates."

Niall Dickson, chief executive of the GMC, said: "We agree with Professor Esmail that there is no room for complacency. We want to work with him. We are duty bound to act where there is evidence of a problem. His report makes a powerful case for action."