Guidance has been sent to members which also suggests practices look at reviewing involvement in practice-based commissioning and refusing non-obligatory new work.
Family doctors should 'stop looking at the top line and start looking at the bottom line', said Dr Stewart Drage of the BMA's GPs committee.
But the NHS Confederation's PCT Network called the move 'shocking' and said it could damage patient care. The 26-page guidance, Safeguarding Patient Services, Maintaining Cost-Effectiveness, said action is needed after the zero increase in GP principals' pay for 2007-08.
It asks doctors to consider stopping local enhanced services, which are 'not properly funded', and directed enhanced services where funding has come to an end.
GPs committee chair Dr Hamish Meldrum said: 'It is a clear message that practices should be doing what has been happening in other parts of the NHS to try and live in their budgets.
'This is to look at the services provided and consider changes to or discontinuation of services that are neither cost effective nor benefiting patients.'
PCT Network director David Stout said: 'We are shocked by the guidance issued by the BMA's GPs committee to its members.
'It is disappointing that the committee is threatening to impact on patient care and derail the NHS improvement programme as part of their pay negotiations.'
Mr Stout added: 'We hope and expect that the majority of GPs won't follow the advice and will carry on working productively with PCTs.'