Hospitals are cynically burying evidence about poor care in a “cover-up culture” that leads to avoidable deaths, and families being denied the truth about their loved ones, the NHS ombudsman has warned.

Ministers, NHS leaders and hospital boards are doing too little to end the health service’s deeply ingrained “cover-up culture” and victimisation of staff who turn whistleblower, he added.

In an interview with the Guardian as he prepares to step down after seven years in the post, Rob Behrens claimed many parts of the NHS still put “reputation management” ahead of being open with relatives who have lost a loved one due to medical negligence.

The ombudsman for England said that although the NHS was staffed by “brilliant people” working under intense pressures, too often his investigations into patients’ complaints had revealed cover-ups, “including the altering of care plans and the disappearance of crucial documents after patients have died and robust denial in the face of documentary evidence”.

Behrens urged ministers to overhaul the way the NHS deals with complaints and how the array of regulatory bodies scrutinise it.

His concerns included that:

• Avoidable deaths were too common, especially in maternity care, mental health and cases of sepsis (blood poisoning).

• The NHS sometimes did “dreadful” and “cynical” things in obstructing families’ pursuit of the full facts about a death, including lying and concealing evidence.

• The service’s legal “duty of candour” was not forcing hospitals to be open when things went wrong.

Although Martha’s rule, which enables families to seek an urgent second opinion if a patient’s condition deteriorates, was a major step forward, bereaved families still struggled to overcome trusts’ reluctance to admit mistakes, he added.

In a plea to the health secretary, Victoria Atkins, and the NHS England boss, Amanda Pritchard, Behrens said: “NHS leaders, including ministers, set the tone for the whole organisation. Time and again we hear that patient safety is a priority, but actions too often suggest otherwise.

“We need to see urgent significant, joined-up intervention to accelerate improvements in culture and leadership, not just in trusts or primary care, but also in NHS England and government.

“Culture is determined not only from the core of an organisation but also from its top leadership.”

The ombudsman voiced alarm at the recurring pattern of hospitals intimidating whistleblowers rather than taking their concerns seriously. He cited University Hospitals Birmingham trust for referring 26 of its medics over 10 years for alleged misconduct to the General Medical Council, which regulates doctors, in an apparent attempt to punish them for raising concerns. None were found to have committed any wrongdoing.

The trust’s board and regulators should have acted earlier to tackle the trust management’s “disgraceful” behaviour, which was well known in the NHS, Behrens said.

The Health Service Journal reported last week how North Tees and Hartlepool NHS trust had been told to pay the surgeon Manuf Kassem £431,768 in damages for racial discrimination and harassment he encountered after he told bosses of his fears that patients had “suffered complications, negligence, delayed treatment and avoidable deaths”.

Last year the same trust had to pay £472,600 in compensation for unfair dismissal to another whistleblower – a nurse – who warned that a patient had died as a result of heavy workloads.

James Titcombe, the chief executive of Patient Safety Watch, who did not get a full explanation for 17 months after his son Joshua died in 2008 of sepsis at nine days old, said he endorsed Behrens’s concerns.

He said research had found that tens of thousands of avoidable deaths occur in the UK every year because safety standards are lower than in other countries.

Paul Whiteing, the chief executive of the patient safety charity Action Against Medical Accidents, said the Countess of Chester NHS trust’s failure to act on doctors’ concerns about the serial baby killer nurse Lucy Letby – including forcing them to apologise to her for doubting her integrity – was an example of Behrens’s charge of “reputation management”.

Last year, a third of NHS personnel during their work saw errors, near misses or incidents that could have hurt staff or patients, according to the latest annual NHS staff survey, he added.

Responding to Behrens, an NHS spokesperson said it was “absolutely vital that everyone working in the NHS feels they can speak up and that their concerns are acted on.

“The NHS has updated its freedom to speak up guidance [and] brought in extra background checks for board members to prevent directors involved in serious mismanagement from joining another NHS organisation.

“As the ombudsman is aware, there have been major efforts to prioritise patient safety in England and progress in creating a more positive safety culture amongst the workforce, which has led to higher levels of patient safety incident reporting than ever before and a widespread focus on improvement, including through the new patient safety incident response framework.

A Department of Health and Social Care spokesperson said: “The safety of all patients is of vital importance, and we have made significant improvements to strengthen protections for patients including publishing the first NHS patient safety strategy.

“We are determined to make the health service faster, simpler and fairer. We are putting record levels of investment into the NHS, and training and retaining staff through the long-term workforce plan to properly resource our NHS for decades to come.”