The GPC's set of 'principles' for GP commissioning, published last week, states that 'wherever possible, consortia should ensure that NHS providers are the providers of choice'.
But Nigel Edwards, NHS Confederation acting chief executive, said GP commissioners should not 'simply dismiss what non-NHS organisations can offer'.
'This principle is doubtful in law and unwise in practice,' he said.
'As commissioners, GP consortia will have a responsibility to purchase the best quality care for patients while also providing value for the taxpayer.
'For profit and not-for-profit firms have played an important role in providing a range of services, including mental health and community services, to the NHS for many years.'
Meanwhile the union Unison has started legal action to block health secretary Andrew Lansley's White Paper reforms, after threatening to do so last month.
The union is calling for a judicial review on the grounds that Mr Lansley's reforms are being implemented without adequate consultation.
Soon after the White Paper was published, NHS chief executive Sir David Nicholson wrote to executives instructing them on how to start implementing aspects of the reforms.
Karen Jennings, Unison's head of health, said the plans represent 'the most fundamental changes to the way the NHS operates since it was created', and must be stopped until the public has been consulted.
A DoH spokesman said it is actively engaging the public and all professions in a series of consultations, and that Sir David's letter was setting out 'first steps' that would not pre-empt the wider consultation.