The BMA survey showed most concerns centre on the powers to be handed to economic regulator Monitor, with 47% of respondents saying this was the most potentially damaging aspect of the reform proposals.
The poll of 940 doctors, which was carried out this month, found that eight out of 10 doctors think the plans are 'unwelcome'.
The BMA said the profession's position on the NHS reforms has hardened.
The poll findings come as the government’s listening exercise is about to draw to a close, with the NHS Future Forum’s report expected early next month.
The government’s plan to overhaul education and training is also a cause for concern, with respondents warning that training standards could slip.
But respondents were generally positive about the proposals for clinically-led commissioning, with 52% of respondents and 55% of GPs welcoming the plans.
GPC deputy chairman Dr Richard Vautrey said the profession’s position on the Health Bill has hardened because many doctors have become ‘fully aware’ of the potential consequences of the reforms.
He said: ‘The BMA had worked hard to ensure doctors are well informed about the possible implications.
‘GPs and other doctors have considered how the new health service arrangements will operate and understand the particular issues around the powers given to Monitor and the NHS Commissioning Board.’