Contracts should be 'revised' regularly to incrementally improve performance, even where there is no underperformance, a DoH procurement guide says.
A DoH spokeswoman confirmed the guidance 'has applications across general practice' but said existing GP contracts would ultimately 'trump' it.
GPC deputy chairman Dr Richard Vautrey said the GMS contract was safe, but APMS and enhanced services contracts could be vulnerable.
NHS Alliance policy lead Dr David Jenner said PMS contracts were 'far more vulner-able' and PCTs were already looking closely at how to prove that inefficient practices have breached their contracts.
The guidance is released amid calls from the NHS Confederation, which represents PCTs, for the power to terminate primary care contracts. The set of guides aims to clarify NHS procurement and tendering rules after health secretary Andy Burnham said last year that 'the NHS is our preferred provider'.
Unions and commentators said the statement signalled Labour's retreat from the use of the private sector. But Mr Burnham told GP in February it meant NHS staff would have a chance to improve before the private sector was brought in.
But the guidance explains: 'We will continue to work with the independent and third sectors, particularly where new services or new service models are required.'
Commissioners must 'continue to remove potential barriers to the participation of non-NHS providers, including access to information systems'.
Dr Jenner said the threat of the commercial sector in primary care 'hasn't gone away' but NHS managers were no longer convinced that the market could solve the NHS's financial woes.
'There is a lot of collaborative and co-operative working at the moment. We are more likely to achieve the productivity challenge that way.'
Meanwhile, MPs warned commissioning may be scrapped because of its high cost. A health select committee report said PCT commissioners were 'too passive' and lack the skills to challenge hospitals, despite reports that up to 14 per cent of NHS funding went on administration and management costs.
The DoH guidance document Commercial Skills for the NHS gives advice on use of the private sector: