It marks a move from the BMA opposing the Health and Social Care Bill to advising members to do something about it, if it receives Royal Assent.
The letter, by Dr Laurance Buckman, chair of the BMA's GPs' committee, describes the Bill as "complex, incoherent and not fit for purpose".
It warns the legislation will be "almost impossible to implement successfully, given widespread opposition across the NHS workforce".
Dr Buckman argued the reforms "will be irreversibly damaging to the NHS as a public service, converting it into a competitive marketplace that will widen health inequalities and be detrimental to patient care", and "could cause irreparable damage to the relationship between GPs and their patients".
Earl Howe, the Health Minister, last night responded by saying the Government was "safeguarding the NHS for future generations".
Although stronger in tone than previous criticisms the BMA has made, the statements in the letter do not change the union's position. It moved to a position of total opposition last November.
However, Dr Buckman also called for GPs to act if the Bill becomes law.
Doctors have become increasingly concerned about the role of private firms in running clinical commissioning groups (CCGs), which will be responsible for buying services for the NHS. These will control about two-thirds of the service's £100+ billion budget.
The Bill contains provisions for private firms to become involved in CCGs, with the Government arguing they will just provide back-office support.
But Dr Buckman wrote: "Unless GPs take an active stand, the day-to-day running of the CCG, and especially its commissioning function, is likely to be outsourced to the hands of organisations providing commissioning support services (CSSs).
"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."
He continued: "We believe 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."
This point is central to much opposition to the Bill, which opponents argue is a poorly-disguised Trojan horse for privatisation of the NHS.
Many GPs favour some sort of clinically-led commissioning - putting doctors in charge of buying health services - but Dr Buckman said the Bill was not necessary to achieve this.
Andy Burnham, the Shadow Health Secretary, described the letter as a "devastating critique of David Cameron's mismanagement of the NHS".
"It is a colossal waste of the NHS's time, energy and money when it should have been focusing on the financial challenge," he said.
Lord Howe defended the Bill. He said: "The BMA's GPC seems to ignore the fact that thousands of GPs covering 95 per cent of the country are already getting on 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.
"Without the Bill we couldn't remove layers of bureaucracy and reinvest £4.5 billion into front-line patient care.
"And the independent NHS Future Forum found broad support for the principles of handing power to doctors and putting patients at the heart of the health system."
The letter follows claims by Andrew Lansley, the Health Secretary, that the Bill was "better" as a result of input from his Liberal Democrat colleagues in the Government.
Earlier this week Nick Clegg, the Deputy Prime Minister, said he had agreed changes that would "protect the NHS from any threat of takeover from US-style healthcare providers".
Mr Lansley told Newsnight: "If there had been a Conservative government, we would have started out in a different place. The bill is better as a result of the Coalition coming together to shape it."
Mr Lansley also claimed: "We've reached the stage where quite a lot of the disinformation out there is a problem, because people are saying things that are literally not true."
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