Private hospitals have been given two weeks to come up with a plan to “get their house in order” on safety and quality or else face tough sanctions imposed by the government, the Guardian has learned.

On Tuesday, Jeremy Hunt will write to the chief executives of 206 private hospitals across England following a damning report into the sector by the safety regulator last month.

The Care Quality Commission found that two in five private hospitals are failing to meet safety standards intended to protect the public from harm, intensifying concerns among ministers over patient safety.

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Thousands of patients are thought to be moved during emergencies to the NHS every year from private hospitals, which rarely have intensive care beds or dedicated resuscitation teams, with the state then left to pick up the pieces.

In a letter seen by the Guardian, the health and social care secretary is calling for fairer remuneration for NHS organisations if they have to deal with the consequences of poor care or mistakes made in the independent sector.

Private healthcare groups are understood to be particularly fearful of the introduction of a compensation scheme for patients who have to be transferred as a result of negligence, as it could hit their profits.

Hunt’s warning comes during a national inquiry into the sector, expected to be published next summer, after the case of Ian Paterson, the breast surgeon who was jailed for 15 years last year for carrying out unnecessary operations in NHS and private hospitals.

In his letter, Hunt threatened those independent hospitals rated inadequate with the same robust and rapid action currently restricted to failing NHS hospitals, including special measures, enforced changes to leadership teams and extra oversight.

Of the 206 independent acute hospitals inspected in the CQC’s first comprehensive analysis of the sector, 62% were given a “good” rating overall and 8% were described as outstanding. However, 30% of private hospitals were deemed to need improvement. Four that were previously rated inadequate had improved.

However, the CQC said it was particularly concerned about safety, with 41% of hospitals rated as requiring improvement in this area and 1% as inadequate. Almost a third were rated as requiring improvement and 3% as inadequate in terms of how well they were led.

Hunt told the chief executives he expected greater transparency when patient safety mistakes had been made, for example by publishing patient outcomes by clinician as well as details of avoidable deaths, bringing the sector into line with the NHS.

The health secretary also called for better governance procedures to make sure private hospitals took responsibility for the work and standards of private consultants, even if they were not technically employees.

Ministers are concerned that some private hospitals currently avoid liability by saying a clinician is not an employee if something goes wrong. They also want clearer processes in place for managing a patient if their health deteriorates in private care and they have to be transferred to the NHS in an emergency.

Hunt wrote: “Like many of my predecessors on both sides of the political divide, I believe that the independent sector can play a useful role in adding capacity, promoting innovation and offering patients choice.

“However, if the sector is to partner with the NHS and benefit from our world-leading medical training, we need urgent assurances that the independent sector will get its house in order on safety, as well as a commitment to take rapid action to match the NHS’s world-recognised progress on transparency.”

Facebook Twitter Pinterest Jeremy Hunt: ‘We need urgent assurances the independent sector will get its house in order on safety’. Photograph: Wiktor Szymanowicz/Rex/Shutterstock

Whitehall insiders told the Guardian that if the providers failed to come up with an action plan within the two-week deadline, the Department of Health would press ahead with developing new policies to clamp down on poor practice without their cooperation.

Some measures could be brought in within weeks but the whole package is likely to take several months to put in place. Health department officials believe they can proceed without legislation as they have a range of other mechanisms at their disposal.

These could include leveraging the independent sector’s reliance on securing NHS contracts and treating NHS patients, as well the CQC’s licensing regime that enables hospitals to practice.

Labour is expected to be broadly supportive of the plan. Jonathan Ashworth, the shadow health secretary, has previously criticised the government for not doing enough to ensure private hospitals are as transparent about the quality of care they are providing as NHS hospitals.

Although the CQC report found most of the hospitals were providing good quality care to patients, the regulator raised serious concerns about safety and leadership.

The commission said the lack of effective oversight of consultants working for these hospitals but not formally employed by them was a major concern. It also found that some private hospitals had failed to learn from incidents and that there was a weakness around reporting. Also that where systems were in place, they were not as robust as required.

One example highlighted operating theatres, where inspectors saw informal practices and instances where the World Health Organization surgical checklist was not being followed rigorously.

The CQC said that where problems were identified, private hospitals were quick to make improvements, but acknowledged that there was still scope for action to be taken to address concerns in vital areas.

The report provided the first comprehensive analysis of the quality of care provided by independent acute hospitals since the CQC introduced an inspection programme in 2015.