Profit-driven firms may oust GPs from their key role in deciding what treatments patients need because of creeping privatisation in primary care caused by the coalition's NHS shakeup, doctors' leaders have warned.

The British Medical Association (BMA) said on Thursday that the relationship between family doctors and patients would suffer irreparable damage and that the reforms would be "irreversibly damaging to the NHS", in its most strongly worded criticism yet of Andrew Lansley's radical reorganisation of the NHS in England.

The BMA denounced the health and social care bill as "complex, incoherent and not fit for purpose, and almost impossible to implement successfully, given widespread opposition across the NHS workforce".

The doctors' union's views are its widest-ranging and most scathing intervention yet in the controversy around the bill, which ministers hope will become law within weeks.

The criticisms come in a letter to 22,000 family doctors from Dr Laurence Buckman, the chairman of the BMA's GPs committee. They reflect both the hardening opposition to the bill among medical organisations and, especially, the growing view among GPs that Lansley and David Cameron's repeated promise that GPs will be the key decisionmakers in healthcare as a result of the changes are a sham.

The letter hints at the possibility of GPs pulling out of clinical commissioning groups (CCGs) – the groups of doctors which will replace NHS primary care trusts from April 2013 – by urging them to take "an active stand" to thwart reforms that, in the BMA's view, would prove ruinous.

Buckman's key criticism centres on the future role of the organisations which will provide commissioning support services (CSSs) to CCGs in the reformed NHS. "These bodies will initially do some or all of the 'back office' functions, but we fear that, in time, they could become the de facto CCG management. CSSs will be required to be outside the NHS as 'freestanding enterprises' and in a market of commissioning support for CCGs as 'customers', by 2016 at the latest," he writes.

"We believe that this will lead to the privatisation of commissioning, destroy the public health dimension to commissioning, with a loss of local accountability to local populations, and is likely to exacerbate health inequalities."

In a fresh appeal for the government to abandon the unpopular bill, Buckman said the BMA would co-operate with efforts to advance the introduction of clinically led commissioning in a non-legislative "alternative way forward" that would build on and spread good commissioning practice.

Andy Burnham, the shadow health secretary, called the letter "a devastating critique of the government's plans. It takes them apart, piece by piece. This illustrates the government's irresponsibility in ploughing on, if they don't listen to this. Dr Buckman is saying that as the profession is overwhelmingly against [the bill], when so much of the reforms depend on the profession, [continuing with the bill] is dangerous," he said.

Doctors were realising that Lansley had made empty promises when he pledged to put them in charge from April 2013, added Burnham. "What we are hearing from GPs, and Laurence Buckman articulates it very well, is that they have been given a false prospectus by the government. At the very beginning the idea was that it would be doctors in control and the more they have seen about how the government is implementing its reforms, the more doctors have felt uneasy and seen that they have been set up to fail."

Buckman's letter also raises another concern – that CCGs would not have the freedom GPs were initially promised. Smaller medical groups supportive of the reforms, such as the National Association of Primary Care and the NHS Alliance, have voiced the same fear recently. Some CCG leaders fear the planned new NHS Commissioning Board, which will oversee the newly-ordered health service from next year, is doing too much to prescribe what they can and cannot do.

Buckman's letter says: "The NHS Commissioning Board, through a new network of bureaucracy, is directing operations from the centre. CCGs do not have the freedom to do much, as their personnel are being proscribed along with their commissioning support services, their structures defined, and their budgets are too small for them to function without uniting into very large and remote units. The ability for ordinary GPs to change things will diminish."

The Department of Health dismissed the BMA's move. "The BMA's GPC seems to ignore the fact that thousands of GPs covering 95% of the country are already getting on with commissioning and improving care for their patients. Patients are being treated in more convenient places, pressure on hospitals is reducing, and we are safeguarding the NHS for future generations," said Lord Howe, the health minister.

"Without the bill we couldn't remove layers of bureaucracy and reinvest £4.5bn into frontline patient care. And the independent NHS Future Forum [launched last year as part of the government's NHS 'listening' exercise] found broad support for the principles of handing power to doctors and putting patients at the heart of the health system," Howe added.

But the Royal College of Nursing, which like the BMA wants the bill abandoned, said: "Today's letter is yet further evidence of the sincere and honestly held concerns that so many health professionals now have about the future of the NHS. Like the BMA, we fear that increased competition could lead to patient care becoming fragmented and that the bill is a huge distraction from the real issue of protecting and improving services at a time when the NHS in England needs to save £20bn," said Dr Peter Carter, the RCN's chief executive.

"We remain convinced that these reforms could damage the very system they were designed to improve and that the outcome will be increased health inequalities. The government needs to act on these concerns and introduce some stability into the NHS as a matter of urgency."

• This article was amended on 2 March 2012. The original said that the NHS Commissioning Board, which will oversee the newly-ordered health service from next year, is doing too much to proscribe what CCGs can and cannot do. This has been corrected.