Doctors face demonstrations outside their surgeries and questions about their high salaries by angry patients because of the government's radical NHS shakeup, the new leader of Britain's GPs warns.

Desperate patients denied life-extending drugs or surgery for their ailments may also vent their frustrations on GPs, because they are due to assume control of deciding how £80bn-a-year of health funding is spent, said Dr Clare Gerada, who takes over tomorrow as chair of the Royal College of GPs.

In an outspoken attack on health secretary Andrew Lansley's NHS reform plans, she also hit out at his decision to transfer responsibility for rationing access to treatment from the National Institute of Health and Clinical Excellence (Nice) and primary care trusts to GPs in England from 2013.

"At worst, the negative impact for GPs could be patients lobbying outside their front door, saying, 'You've got a nice BMW car but you will not allow me to have this cytotoxic drug that will give me three more months of life,'" Gerada told the Guardian in an interview.

"I'm concerned that my profession, GPs, will be exposed to lobbying by patients, patient groups and the pharma industry to fund or commission their bit of the service. There could be letters from MPs and patient groups, and begging letters from patients."

Making GPs "the new rationers" of NHS care could ruin the long-established bonds of trust between them and their patients, undermine "the sacredness of the consultation" and turn patients into little more than "customers" who shop around trying to get the best treatment for their ailment, Gerada added. Inherent conflicts of interest in the new system could also jeopardise GP-patient relationships, she warned. "Patients might think that the decision made about their healthcare will be based on self-interest – GPs saving money for themselves rather than spending it on patients." Certain treatment decisions, and a GP consortium's need to balance its books "could be misconstrued".

The NHS will not survive intact Lansley's plans to scrap many existing NHS bodies, introduce GP commissioning and push through greater competition between hospitals, she predicted.

"I think it is the end of the NHS as we currently know it, which is a national, unified health service, with central policies and central planning, in the way that [Aneurin] Bevan imagined," said 51-year-old Gerada, who represents Britain's 40,000 family doctors. Lansley's shakeup will lead to a much greater role for private healthcare companies, the likelihood that England's health system will look more and more like America's, and GPs being blamed for things such as the NHS's inability to cope with a winter crisis, long waiting lists and the decommissioning of services to save money, she added.

GPs in their new role will bear the brunt of the NHS's need to save £20bn by 2014, which will lead to far more "postcode lotteries" in services such as IVF, expensive drugs, and even access to particular hospital specialists such as surgeons and gynaecologists. Leaving each of the new GP consortiums to decide individually what treatment should or should not be available locally will lead to disputes over access to care. "I don't understand why he's putting in a system that in Scunthorpe you can get a different service to Scarborough, when we've spent the last 60 years working against that", said Gerada. Her comments are the most detailed criticism yet made by any senior doctor of Lansley's plans, which have caused serious unease among medical organisations.

John Healey, Labour's shadow health secretary, used them to portray Lansley as dogmatic and out-of-touch. "These criticisms from an influential GP again reveal how Andrew Lansley is failing to listen to the warnings of doctors, nurses and health experts to slow down on his high-cost, high-risk plans," said Healey.

"With plans for the biggest reorganisation in the NHS's history, it is also becoming clear that he is running a rogue department, operating in isolation from his colleagues in government."

Healey echoed Gerada's concern about patients in future questioning GPs' motivations. "Patients will worry about treatment decisions – are they being taken in their best interest or the best interest of the GP consortium's budget?"

The British Medical Association warned the changes could see the NHS fragment. Dr Laurence Buckman, chairman of the BMA's GPs committee, agreed with some of Gerada's concerns. "GPs are fully aware of the difficulties facing the NHS as we enter a very difficult financial period and that tough decisions will have to be taken. The BMA has repeatedly expressed its concerns about the timing of the white paper proposals as well as the potential risks and benefits that may result from the government's plans," he said.

Prof Chris Ham, chief executive of the King's Fund health thinktank, endorsed Gerada's view that Lansley should move more slowly. "With international evidence this week showing our health system performing well compared to other countries, and the NHS facing significant financial pressures over the next few years, evolutionary change building on existing arrangements offers a more promising route to improving the NHS than radical structural changes," he said.

A Department of Health spokeswoman said: "Our reforms will indeed mark a new era for the NHS – one where patients and clinicians are at the heart of the service. Our reforms aren't an option, they are a necessity in order to sustain and improve our NHS. The reforms are far-reaching but they also build upon existing designs. We share a common goal with the RCGP that we all want patients to get the best health and care services."

But she added: "We understand concerns around implementation. That's why we have consulted extensively on our plans, and have already announced a programme where GP consortia can start testing white paper principles. We will announce the outcome of the consultation later this year. We believe that both purpose and pace are vital to improve services for patients."