Many hospital wards need to be closed and whole departments moved elsewhere so the NHS can improve care for the most seriously ill patients, the new leader of the UK's 200,000 doctors has warned.

Professor Terence Stephenson, chair of the Academy of Medical Royal Colleges (AoMRC), wants ministers and NHS bosses to downgrade the status of some hospitals and push through major rationalisation of key services such as major surgery or intensive care, despite local campaigns to save units.

The academy is the voice of the UK's medical royal colleges and represents groups of specialist doctors such as GPs, hospital physicians and surgeons.

Speaking to the Guardian in his first interview since being elected, Stephenson said it was "wasteful" of NHS resources that so many hospitals, often only a few miles apart, provide exactly the same services. Acute medical services should be concentrated in fewer, bigger, more centralised units, so that care teams would increase their skills by treating more patients, even if that means some entire hospitals closing as a result, he added.

"We do try to deliver care too broadly across too many centres. We're trying for that aphorism that everybody wants open heart surgery in a cottage hospital. It's just not deliverable. I don't think it's possible in quite a small country of 60 million people to have 200 to 300 24/7 acute centres offering every single discipline", said Stephenson.

The NHS is hamstrung by having many of the same hospitals it had when it was created in 1948 and the plethora of hospitals providing identical services explains why patient outcomes are not as good for certain types of NHS care as in European countries such as France and Germany, despite significant extra investment since 2000, he said.

Centres of expertise should look after patients needing hi-tech care, risky treatment or with rare or complex conditions, with local hospitals losing their ability to treat such cases as inpatients and instead dealing with common, less serious conditions.

When London reorganised trauma services, for example, "nobody really dissented hugely with the idea that you can't treat people who have had major car crashes in every small hospital, that you would transport them into major centres", said Stephenson.

Research done by the Royal College of Paediatrics and Child Health, of which Stephenson was president until May, concluded that the NHS's 220 specialist paediatric units should be reduced to 170. The same rationale applies to adult hospital services because "many of these small hospitals admitting key patients are quite close to another or slightly larger hospital".

Combining two units onto one site is easier in urban areas as the distance between hospitals in rural areas makes centralisation there impractical, he added. "Whether they close or not would be down to geography. If they are three miles apart people can have care close to home so I wouldn't go to the ditch to keep every single hospital open," said Stephenson.

His outspoken comments will increase the already growing pressure on ministers to oversee a slimming down of the hospital sector. Sir David Nicholson, the NHS chief executive, last month called for radical changes in healthcare, including hospital closures, and for politicians to be "honest with the public about the nature and scale of the change that's required".

The former Conservative health secretary Stephen Dorrell, who chairs the Commons health select committee; the NHS Confederation, which represents NHS managers, and the influential King's Fund health thinktank all favour widespread reorganisation.

Dr Tony Falconer, the president of the Royal College of Obstetricians and Gynaecologists, argued recently that up to a third of maternity units in urban areas should close in order to improve the health of mothers and babies.

But individual closures are regularly the subject of campaigns backed by local MPs. On Sunday thousands marched in Leeds to campaign to save the children's heart surgery centre at Leeds general infirmary, which is being recommended for closure in an NHS review. They were joined by Labour shadow ministers and local MPs Ed Balls, Yvette Cooper, Rachel Reeves and Hilary Benn.

The coalition's controversial NHS reforms in England will increase the chances of units disappearing because the GP-led local clinical commissioning groups that will gain control of £60bn of the NHS budget next April will send patients to where is best, rather than necessarily their local hospital, Stephenson added.

The drive to deliver more NHS services outside hospitals, closer to patients' homes, would also hasten the process, he said. "Some wards will close and that's not the end of the world," he said, as long as patients could be assessed locally and sent to a centralised specialist unit if necessary.

Doctors need to play a leading role in persuading a sceptical public why radical changes to the way the NHS provides care is necessary, as they have done over the recent controversial NHS review called Safe and Sustainable, which will see England's collection of 11 centres performing heart operations on children shrink to seven, added Stephenson.

Similarly, when maternity care in Greater Manchester was reorganised, with four of 12 hospitals losing their unit, "part of the reason that was successful was because doctors and nurses were fairly candid about saying 'we think the quality of your care is not as good as it could be,'" Stephenson said. "If the message coming from local politicians, doctors and nurses is that the care right now is fantastic and is being stripped away to save money, then of course you will have people campaigning.

"If the message, as with Safe and Sustainable, is actually 'to be honest, we're ashamed to say that the care of people isn't as good as it could be and we could make it better this way,' I think you could take the public with you," he added.

Stephenson's dramatic intervention divided opinion in the NHS. Professor Steve Field, the chair of the government's advisory NHS Future Forum, said he was "absolutely right". The NHS must replicate the centralisation of stroke care in London from 32 hospitals to eight hyper-acute stroke units, which is believed to have saved 400 patients a year because far more now receive clot-busting drugs, he said.

MPs, who usually oppose the loss of any local unit, "need to understand that these are difficult decisions but they need to be made and the NHS is inevitably going to have more of these decisions to make in the next few years", added Field, the former chair of the Royal College of GPs.

Mike Farrar, chief executive of the NHS Confederation, said the NHS would be "unsustainable" unless care was radically reshaped so the NHS could properly treat the growing numbers of patients who are old or have a long-term condition.

"Senior clinicians have sometimes been reluctant to step forward and yet they carry so much weight with the public. But I think the tide is turning. There is an emerging coalition of managers and clinical leaders who understand the need to speak up because if we don't the NHS will be unsustainable," said Farrar.

Cabinet ministers William Hague and Iain Duncan Smith have backed local campaign groups protesting about proposed downgrading of NHS facilities affecting their constituents. But ministers need to "have the courage to do the right thing for patients" by backing greater centralisation, said Farrar, who praised the health secretary, Andrew Lansley's recent "decisive action" over the financially ailing South London healthcare trust as an example of ministers taking a difficult decision.

"More broadly, ministers should explain the [reconfiguration] issues clearly to the public and help create the context in which more radical change can happen. Otherwise, the NHS will be fighting pitched battles around the country for the next decade," said Farrar.

"It is really significant that the Academy is now ready to help persuade the public of the importance of these issues."

A Confederation survey last month of 252 chairs and chief executives of 200 healthcare providers such as hospitals and primary care trusts found that 31% back greater concentration of specialist services, 28% believe whole hospitals should close and 15% favour closing some services.

But health unions voiced disquiet about hospital services being merged. "When the evidence is there, change within the NHS is vital in maintaining the provision of high-quality care to patients, but Unison would always caution against change for changing's sake," said Christina McAnea, head of health at the union, which represents 400,000 NHS staff.

"Health service professionals are still getting to grips with the rudiments of the Health and Social Care Act, so we would question the wisdom of introducing yet more wide-scale reform without broad and conclusive evidence to support it."

Rachael Maskell, head of health at the Unite union, warned centralisation of services could see patients being cared for far from home and and relatives facing long journeys to visit them. "There is also the clinical and social needs of patients. There is no point having patients who are miles away from friends and family, isolated in a hospital, because there is one national centre for a service," she said.

Local multidisciplinary teams of NHS staff, not just doctors or ministers, should decide which services hospitals provide, she added.