The treatment provided by hospitals and GPs is so "dangerously" variable that poor care kills up to 10,000 patients a year, the head of the NHS regulator claims.

In a withering criticism of standards in the health service, David Prior, the chair of the Care Quality Commission (CQC), warns that "many patients receive poor care".

This leads to "many thousands" of patients dying avoidably every year, an unacceptable situation that threatens the NHS's integrity, he said.

Prior's scathing remarks risk being seen as NHS bashing by staff and appear to show that he believes too little has been achieved since the Francis report 18 months ago into the Mid Staffs scandal triggered a blizzard of moves to improve care and safety.

The leader of Britain's doctors rejected Prior's assertions and said he was not representing the true picture, which is that most patients get world-class care.

Prior launched his scathing attack on the NHS in an article for Wednesday's Guardian. In it he claimed: "Any assessment of the NHS can only have one possible conclusion: standards of care are highly variable, sometimes dangerously so.

"We have some outstanding hospitals, we have some inadequate hospitals. And the variation in primary care between different GP practices is probably even greater."

Of the 40 hospital trusts in England that CQC inspectors have visited since March under a much more robust and inquisitive new inspection regime, five were rated "inadequate" – the lowest ranking.

Prior was the Conservative MP for North Norfolk from 1997 to 2001, chaired the board of Norfolk and Norwich University hospital trust from 2002-06 and is also an ex-chairman of the Tory party. He was appointed by the government to lead the CQC in January 2013.

Explaining the risk posed by variation in the quality of NHS care, Prior added: "This variation matters not just because many patients receive poor care; indeed many thousands die avoidably every year. No one knows how many, but in hospitals it has been estimated to be anywhere between 3,000 and 10,000 – not a statistic that any other area of human activity would be happy with.

"It also matters because variation strikes at the heart of the NHS and its core principle that everyone should receive good quality care free at the point of delivery. In fact they do not."

Prior's estimate of up to 10,000 deaths a year is actually lower than that cited by Jeremy Hunt, the health secretary. He has claimed that NHS staff cause around 12,000 deaths annually and that "utterly, utterly shocking [things] are happening week in, week out in our NHS", such as feeding tubes being put into a patient's lungs instead of their stomach.

But Dr Mark Porter, chair of council at the British Medical Association, rejected Prior's claims. While action must be taken to ensure safety if poor care is uncovered, "the vast majority of patients receive world-class care despite the NHS being under enormous pressure from rising patient demand and falling resources".

Porter also dismissed as "ideologically driven" Prior's comment that poor care was tolerated in the NHS because of its "monopoly" and belief that a competitive market would force it to improve standards.

"There is no evidence that introducing a market system into the NHS will make any real difference to patient safety and recent reforms as part of the Health and Social Care Act that have attempted to increase competition in the NHS have actually damaged the way care is delivered", said the BMA leader.

However, the CQC's forthcoming annual report, called State of Care, is understood to include findings that support Prior's claim about too much care being "dangerously" variable.

Hunt appeared relaxed about Prior's article, despite his determination to show that care is being improved.

A spokesman for the health secretary said: "For too long poor care in the NHS was swept under the carpet which resulted in the tragedy we saw at Mid Staffs under the last Labour government. The role of the CQC and the new chief inspectors is to root out poor care wherever they find it without fear or favour.

"This is in the best interests of patients and NHS staff and allows problems to be confronted and addressed quickly."

He added: "Our response to Francis has already seen five hospitals that were put in special measures turned around and the CQC inspection regime is driving up the performance in many more."

NHS England also rejected Prior's criticism. Jane Cummings, its chief nursing officer , said: "The NHS treats millions of people every year and the overwhelming majority of our patients receive great care from staff who are pulling out all the stops. We do need to do more, but the quality of care is better now than at any point in the history of the NHS."