Only one in 100 prisoners who make an allegation of discrimination against staff has their case upheld, according to new analysis which claims that the system for handling complaints of racism and bigotry in the penal system is neither fair nor impartial.

By contrast, three-quarters of staff who alleged discrimination by an inmate had their complaint upheld.

As prisons struggle to cope with escalating levels of violence and fewer officers, the report by the Zahid Mubarek Trust and the Prison Reform Trust reveals that the equality within jails is becoming less of a priority.

The analysis of 610 investigations from eight London prisons during 2014 is the first formal study of the use of the discrimination incident reporting form (DIRF) in prisons since its introduction more than five years ago. The DIRF was brought in after a review into how incidents of racial discrimination were handled by the prison service following the death of Zahid Mubarek, murdered by his racist cellmate 17 years ago.

The report, published on Sunday, warns that the threshold of proof that prisons use to test allegations from inmates is often too high, meaning that evidence suggesting discrimination was often easily dismissed. In about a quarter of the claims, the explanation for dismissing the allegation was weak, says the report, often merely stating “no evidence of discrimination”. The authors claim the system was not equipped to tackle subtle forms of discrimination, for example when prisoners reported routine favouritism the vast majority of allegations were dismissed.

Other findings show that nearly three-quarters of staff claims were upheld compared to only 8% of prisoners’ discrimination reports. One in five complaints made by staff were used as a way to defend themselves from allegations of bias from the prisoners, says the report, even though prison policy states that prisoners who allege discrimination should not face recriminations. The majority of prisoner complaints were about race (62%) followed by religion (15%) – with a third of these about Islam – and disability (10%), with verbal abuse the most common reason for alleging discrimination. The report found that despite the Equality Act in 2010 binding prisons to eliminate unlawful discrimination, harassment and victimisation, serious issues still remained.

“Black prisoners are over-represented in segregation units, more likely to have force used against them, and more likely to be on the basic regime. Muslim prisoners are more likely to say they have been victimised by staff. And both groups are less likely than their white counterparts to believe that officers treat them with respect,” the report says.

Around a quarter of prisoners are from a minority ethnic group, compared to 14% of the general population, with more than a third of inmates estimated to have a physical or mental disability compared to 19% of the public.

Prime minister Theresa May has vowed to tackle discrimination in the justice system, and an independent review into the treatment of black and minority ethnic people in prisons, chaired by David Lammy MP, is due to report this summer.

Peter Dawson, director of the Prison Reform Trust, said: “The fact that the prison service allowed this study is testament to its desire to learn from independent scrutiny, but the findings in this report show widespread failings in the complaints process. It is simply not credible that virtually every complaint of discrimination made by a prisoner about staff is false, when we know as a matter of fact that many minority groups in prison routinely experience disproportionately negative outcomes.”

Imtiaz Amin, director of the Zahid Mubarek Trust, said: “This disturbing report shows that the system is still failing to hear and to respond effectively. Being held to account is a cornerstone of fairness, and essential to a safe and decent prison operation. Handling prisoner complaints properly – and analysing what they say about the prison’s health – is core business, and there is much to put right.”

The report recommends that the prison service should strengthen the process for investigating claims of discrimination. Investigations should make greater use of problem-solving, mediation and outside expertise to address the problems that gave rise to the complaints. In addition, a prison equality advisory group should be established to advise on policy.

Commenting in the foreword to the report, the former chief inspector of prisons, Lord Ramsbotham, said: “From the evidence in this report it is clear that, despite the policies to tackle racism and discrimination, introduced following Zahid’s death, the focus, energy and accountability to deliver equality have slid backwards.”