The Bill gives economic regulator Monitor powers to enforce competition law on consortia, which could trigger legal action against GPs who discuss services with hospital staff, the GPC fears.
GP leaders also warned that the NHS Commissioning Board has been handed 'absolute power' to 'command and control' GP consortia.
The Bill, published last week, sets out the legislative framework for health secretary Andrew Lansley's NHS reforms.
GPC deputy chairman Dr Richard Vautrey said the BMA will challenge the powers given to Monitor.
'We have concerns about any mechanism that prevents collaboration between GPs and consultants,' he said.
'Regularly discussing services with hospital colleagues could be seen as anti-competitive and result in legal action against GPs.'
Dr David Jenner, GMS/PMS lead at the NHS Alliance, warned that the Bill paves the way for the NHS Commissioning Board to exert 'stifling pressure' on GP consortia to make immediate savings.
The Health Bill also makes clear that the NHS Commissioning Board can sack a GP consortium's accountable officer, disband it, vary the area it covers, force it to take on or remove practices, or strip it of functions if it underperforms.
'If they don't rapidly save cash, they could be issued with directives on how to operate by the board,' said Dr Jenner. 'The rhetoric is all about freedom but this is very much command and control.'
Defending the Bill, Dr James Kingsland, DoH national clinical commissioning network lead, said the NHS Commissioning Board must have the power to change consortia's behaviour if they are failing.
The Bill proposes that consortia publish annual performance data and annual plans.
It confirms that the NHS Commissioning Board can top-slice consortia funding to create contingency funds and pay bonus payments up front if they expect strong performance.
Reports published with the Health Bill estimate the cost of the reforms at £1.5 billion over three years.
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