Hospitals will shut, others will lose their accident and emergency or maternity units, and some will be downgraded to glorified health centres because of the government's NHS shakeup, the head of England's leading hospitals has warned.

Sue Slipman, chief executive of the Foundation Trust Network, told the Guardian that handing GPs control of £80bn of NHS funds, letting private healthcare firms provide treatment and giving patients more choice about where they are treated – key policies promoted by the health secretary, Andrew Lansley – would increase existing pressures on hospitals so much that some will not survive.

"There will be some 'shut' signs; I suspect there will be some closures. There will be fewer A&E departments and in urban centres there may well be fewer maternity units," said Slipman, who predicted unprecedented changes to hospitals over the next few years.

Cities, especially London, will experience the greatest loss of hospital facilities, she believes, while local hospitals in rural areas are more likely to continue to offer a traditional wide range of medical services.

Slipman – who represents large, successful hospitals that are semi-independent of NHS control after gaining foundation trust status – said widespread "rationalisation" of hospitals was necessary, and would ultimately lead to better care for patients.

"The NHS is not sustainable in its current form, including [its] supply of hospitals," said Slipman. "If you want to retain a service that's free at the point of delivery, it has to be the most efficient it can be and produce good quality. Whatever you think of these [Lansley's] reforms, you cannot be against reform if you want a sustainable NHS in the long-term. The reconfiguration of certain services is just the rational outcome of that change."

But she conceded that patients' attachment to particular hospitals, and the rivalry between health professionals, mean the changes will be "difficult and controversial". She added: "This debate is the most difficult area [in healthcare]. On the whole, politicians don't like it. You'd be a very brave politician to stand up and say 'we need service reconfiguration', even if that's the logical policy."

But the radical restructuring of the NHS foreshadowed in the health and social care bill will inevitably lead to what Slipman called "significant" changes and "a lot more" reconfiguration.

Hospitals are already under pressure from an ongoing drive to shift healthcare into GPs' surgeries and other community settings. Financial pressures linked to the NHS's need to save £20bn by 2015 and its flat, or even reduced, budget in the coming years, are also causing difficulties.

From 2013, GPs will be able to decide which hospitals to arrange treatment contracts with. This will hand them "the ability to destabilise" local hospitals and is likely to lead to "huge commissioner-driven reconfiguration of services", Slipman said.

Allowing private firms to compete with the NHS for patients would add to the pressure on the viability of individual units and entire hospitals. The capital will be hardest hit, she predicted: "London proportionately has more hospitals per head of population than elsewhere, and that level is unaffordable in the new world."

Slipman added that the public should get used to the idea of some current hospital buildings offering little more than outpatient clinics, with services such as A&E, surgery and acute medicine increasingly concentrated in fewer places, including regional centres of excellence in treating major conditions.

The NHS may even see the emergence of "national chains" of hospitals, in which financially sound, clinically proven hospitals take over struggling smaller ones, some of which could operate on what Slipman called "the Debenhams model". The main hospital's name would adorn the building but services could be provided by a range of other hospitals – like rival outlets' concession stores inside Debenhams branches.

Dr Clare Gerada, chairman of the Royal College of GPs, said changes in the NHS should be driven by what places offered patients the highest standard of treatment, and not by a fixation with the bricks and mortar of local hospitals – even if that meant that some hospitals were "culled".

A Department of Health spokesman said: "We do not agree with this bleak outlook. We are passionate about improving care for NHS patients, and that's what our plans will do."

Polly Toynbee, page 28