The NHS was accused tonight of suppressing a damning report that found Mid Staffordshire-type failings at a pioneering centre for rape victims.

The confidential report, obtained by the Bureau of Investigative Journalism for The Independent, found basic forensic protocols were routinely breached at the London centre, which was set up to provide a “gold standard” in support for rape victims, and to improve conviction rates.

Dozens of samples taken from victims of sexual attacks that should have been sent for forensic analysis were found left in a fridge, according to the report, which also exposed “multiple deficiencies” in the unit’s dealings with children and vulnerable adults.

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Staff at the unit described working in “an oppressive, tense environment” and told investigators that they dreaded their shifts but were afraid to complain to managers.

The report concludes that many of the problems “echoed the underlying failures identified” as part of the inquiry into the Mid Staffordshire scandal. But until now the report, commissioned by Barts NHS Trust into the “whole system failure” at the Whitechapel Haven, has not been made public – despite the unit’s temporary closure after the problems came to light last year.

Tonight Barts, which ran the Whitechapel centre, apologised for the “inexcusable failings” but insisted it had not attempted to hide the problems identified in the report.

But Liz Kendall, Labour’s shadow care minister, said: “The women who have been affected have a right to know who is responsible for [these failings] and that they are properly held to account.”

Baroness Jones, London Assembly member for the Green Party and former mayoral candidate, said the failure to publish the report promptly gave the impression that “what had happened at Whitechapel was covered up”.

Whitechapel is one of three rape centres set up in the capital in 2000 where women can be seen by specialist doctors, receive treatment for injuries and emergency contraception, and be referred for counselling and other support.

The centre was jointly funded by the NHS and the Metropolitan Police Service – which refers women to the centre for specialist support and relies upon it to collect forensic samples for use in potential prosecutions.

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The NHS investigation, completed in April 2013, was prompted by concerns about the standards and practices at the Whitechapel unit which had led to its closure for four months in 2012.

A copy of its report, obtained by the Bureau of Investigative Journalism following a Freedom of Information request, reveals widespread inadequacies in the collection and storage of forensic evidence from rape victims. It found:

* Samples from 93 alleged rape victims had not been passed on to the police forensic service for analysis.

* The unit had a grubby examination suite that “did not meet the standards required in terms of a safe forensic area”.

* Criminal exhibits were stored in plastic bags, which can cause evidence to deteriorate, and contaminated clothing was mixed with clean items.

The report reveals that when two members of the investigation panel visited the centre to assess how the service was being run they found “a general air of grubbiness”.

Concerns raised by the Department of Health had not been acted on and were “treated in a dismissive manner”, the investigators also found. Inside the unit no one was accountable for the quality of patient care, with the lead clinician “either unable to take leadership or not suitably qualified or experienced to assume this role”.

The report concludes that many of the problems identified at Whitechapel were the same as those identified by Robert Francis in his inquiry into what went wrong at Mid Staffordshire.

“The information gathered echoed many of the underlying failures identified in the Francis report in terms of clinical standards, clinical governance, accountability, training and staff failing to effectively raise their concerns,” it said.

The centre has reopened but with a reduced service. Responsibility for its management moved to King’s College Hospital NHS Foundation Trust in April this year.

An NHS England spokesman said that after the investigation, two members of staff had been dismissed. Victims directly affected by the problems identified at Whitechapel have been contacted, he added. “They received a full apology and were invited to make an appointment with a trained counsellor to receive the results and continued support,” he said.

In a statement Barts NHS Trust said: “We are extremely sorry for the inexcusable failings at the Whitechapel Haven. As soon as we became aware that there was an issue in 2011, we took swift and immediate action to ensure that all the affected samples were re-tested and contacted the individuals involved to offer a full apology, support and counselling.”

The statement added that the trust had shared the findings of its investigations with doctors at King’s College Hospital and that the report would be discussed at an NHS England meeting in February.

“The Trust has strived for transparency throughout and the independent investigation report commented on the diligence, honesty and openness of our staff in working together to discover and correct what had gone wrong.”

All the havens are now under the control of King’s College Hospital. In a statement it said: “Since April, we’ve worked hard to drive forward improvements across the entire service. This includes establishing new systems of governance to improve the auditing and management of samples.”

* The number of rape files passed by the police to the Crown Prosecution Service for criminal proceedings is a third less than it was three years ago, new figures suggest.

Figures uncovered by Labour show that police in England and Wales passed 5,404 rape cases to the CPS in 2012-13 for it to decide whether to charge alleged offenders – compared with 8,100 in 2010-11.

The London havens: ‘One-stop shops’ for victims of sexual assault

The three London Havens are specialist sexual assault referral centres. The first one (Camberwell) was established in 2000 to reduce the time victims had to wait before a forensic medical examination could be provided and to be a “one-stop shop” where they could be seen by specialist doctors, receive treatment for injuries and emergency contraception if necessary and be referred for counselling and other support.

The Havens accept assault victims who have been raped up to a year previously, though forensic evidence is only useful if gathered in a “forensic window” considered to be up to seven days after the attack. There are three Havens: at Whitechapel, Paddington and Camberwell. Since April 2013 Kings Healthcare Trust has managed them all.

The three Havens cost £4.33m to run and are jointly commissioned by the Mayor’s Office for Policing and Crime, working with the Metropolitan Police, and the NHS. The Met’s contribution for 2013-14 was reduced by £216,500 because of an underspend resulting from the temporary closure of Whitechapel in 2012-13.

NHS England has so far failed to answer questions about whether it received a similar discount.