The coalition's NHS shakeup could destroy the trust between GPs and their patients by making family doctors responsible for the rationing of treatment, the leader of the medical profession has warned.

GPs would be at risk of being seen as "agents of the state" who are implementing government cuts once the historic change in their role takes effect on 1 April, Dr Mark Porter told the Guardian.

Porter, chairman of the ruling council at the British Medical Association (BMA), said doctors were worried that their role in deciding which patients got access to which treatments, as a result of the formation of 211 GP-led clinical commissioning groups (CCGs) across England, would prove divisive and unpopular.

CCGs replace primary care trusts, comprising NHS managers who had the final say in what care patients received, and will control £65bn of NHS funds this year.

"CCGs will be the new rationers of care. This concerns doctors because they are very uncomfortable with having to take rationing decisions," Porter said. "The General Medical Council's 'duties of a doctor' says the first one is to make the care of your patient your first concern, and we're being dragged away from that."

While most doctor-patient relationships would be unaffected by the restructuring of the NHS, he said, "the risk is there that what will creep into it is the thought in the patient's mind that the doctor's recommendations or decisions have not been based on the patient's best interests but on some local policy which restricts the NHS there rather than somewhere else.

"But when you bring that sort of thing into the doctor-patient relationship, it destroys the trust that is so important for being able to successfully work with the patient to manage a condition. So the GP‑patient relationship could be threatened," said Porter.

GPs, who often top polls of most trusted professionals, could see their reputation harmed by such a difficult role, which Porter blamed on government underfunding of the NHS. The overhaul has created hundreds of local and national NHS organisations. "Doctors are being asked to be agents of the state in implementing public-sector resource restrictions," he said.

The NHS's duty to make £15bn-£20bn of "efficiency savings" by 2015 through rationing access to procedures such as IVF, cataract removals and exploratory knee operations was likely to be extended to other procedures by CCGs as more savings had to be made, added Porter.

MPs on the Commons public accounts committee said last month that patients were paying the price of the savings drive as NHS bodies sought to restrict entitlement to care rather than money-saving innovations.

Porter said the need to save money had become so great that some hospital doctors could not simply "cross-refer" – ask a colleague in another speciality to examine a patientabout whom they are concerned, – without the PCT first approving it, a break with the tradition of consultants' judgment being trusted.

Until now, only GPs have been subject to trusts using such "demand management" mechanisms for patients who doctors want to send for examination at a local hospital.

Katherine Murphy, chief executive of the Patients Association, endorsed Porter's warning and said disputes between GPs and patients over restrictions on treatments were unavoidable in the new era.

"The relationship with patients and their GP is unique. Patients place their trust in their GPs and their decisions around care. We are concerned that the creation of CCGs will fundamentally alter this relationship between patients and their doctors, with breakdown relating to funding decisions almost inevitable," she said.

CCGs' responsibility to stick to their budgets could cause further problems, she added. "Will the GP always act in the best interest of his/her patient or will he put the finances of his organisation first? Will patients have the most appropriate investigations undertaken at the right time and will National Institute for Health and Clinical Excellence-approved drugs be prescribed, or will we see a huge rise in the postcode lottery of prescribing?", she said. GPs and CCGs face "a temptation to put economics and business principles ahead of quality and safety in patient care", Murphy added.

Mike Farrar, chief executive of the NHS Confederation, which represents hospitals and many CCGs, said the new NHS set-up was "a big opportunity to improve care and the way things work. The clinical expertise of commissioning organisations will be a huge asset and we need to take full advantage of it."

However, he added, the service's tough financial position – "coping with a flat budget and rising demand and costs" – represented its biggest challenge. "Organisations have a tough job on their hands to continue providing quality care within a much tighter financial envelope."

A Department of Health spokesperson said: "There are already examples up and down the country of the new GP clinical commissioning groups improving care, all being achieved because care is being directed by the healthcare experts who know patients best.

"We have always been absolutely clear that b eing efficient does not mean cutting or rationing services – it means getting the best value for every pound the NHS spends.

"The NHS has done well to see more patients, reduce the number of patients waiting over a year to start treatment and remain on track to save over £5bn this year. Any NHS underspend will still be available for NHS organisations to ensure high-quality, sustainable health services are delivered to patients now and in the future.," the DoH said.