Sandra Haynes-Kirkbright was treated unfairly by the Royal Wolverhampton NHS Trust which runs New Cross and Cannock Chase Hospitals, it said.
The trust showed a lack of governance and proper management at senior levels, an independent inquiry has found.
And the trust's investigation into claims of malpractice was 'significantly flawed'.
In fact, instead of starting an internal probe, the report says chief executive David Loughton told two directors to 'ensure' Mrs Haynes-Kirkbright's concerns 'did not interfere' with an inspection by health watchdog Monitor.
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Now, a review of 'governance' will be carried out to raise management standards at the Royal Wolverhampton NHS Trust.
Mrs Haynes-Kirkbright worked as head of clinical coding and data quality at the trust, having joined from Stafford hospital.
Mrs Haynes-Kirkbright's job involved recording details of the care patients received. It did not require medical qualifications.
She said disciplinary proceedings were launched against her after she reported concerns about malpractice at the New Cross-based trust. She had claimed 'every rule in the book' was broken to improve official mortality rates and compared conditions to scandal-hit Stafford Hospital.
She said she had complained to various senior figures but added: "I told them and they just said don't worry your little head about it."
Her allegations and treatment sparked an investigation by the NHS Trust Development Authority, using independent consultants Verita. The report was completed in 2015 but only released yesterday after legal wrangling.
Mrs Haynes-Kirkbright claimed she had been head-hunted to 'fix' mortality rates and alleged she was suspended after she refused to take part in a cover-up. The report found:
The trust investigations of Mrs Haynes-Kirkbright's whistleblowing allegations were 'significantly flawed'
Mrs Haynes-Kirkbright was not treated fairly by the trust
Examples were found of the trust not having followed due process in its policies and procedures and the legislation in investigating and handling the allegations by and about Mrs Haynes-Kirkbright
Evidence of a lack of governance and proper management at senior levels
An independent governance review of the trust is now being commissioned by NHS Improvement to examine issues raised.
The report did not seek to prove the allegations, merely looked into the way they were handled. Last night, the Royal Wolverhampton NHS Trust, said: "We acknowledge the findings, none of which are related to patient safety, care or experience.
"The report relates to events from over four years ago. It does not reflect adequately the significant information provided by the trust to Verita.We take whistleblowing seriously and would always encourage any member of staff, or patient, to come forward. We have reviewed our whistle-blowing procedures and policies and have had a new HR leadership team in place since 2014."
Mrs Haynes-Kirkbright, who is from Texas and now lives in Silkmore, Stafford, responded to the report, saying she was pleased her concerns had finally been listened to.
She has been suspended on full pay from her £54,000 job since 2012. The internal disciplinary charge against her is still outstanding.
She said her reputation had been damaged, adding: "I had plans about where my career would go, I don't have any plans now. I'm still employed there I believe, I don't want to speculate or second guess what happens next."
The report says Mr Loughton, knew of her concerns over coding irregularities by 20 April, 2012. It states: "He did not, as he should have, initiate a whistleblowing investigation. Rather, he instructed two of his executive directors to ensure that her concerns did not interfere with the Monitor visit."
Mrs Haynes-Kirkbright was suspended in July 2012 because of allegations made against her by colleagues of bullying, harassment, persistent swearing and unprofessional behaviour. Fran Steele, of NHS TDA, said: "We have commissioned a governance review to support the trust in developing leadership and oversight of governance across the organisation."