Dr Clare Gerada said that cuts were increasingly undermining practices' viability. Data from medical accountants revealed by GP last month showed the decline in GP funding was accelerating.
Dr Gerada warned that 'it won't be very long' before some practices are forced to become outpatient services of foundation trusts to survive.
Senior GPs backed calls for CCGs to be able to invest in strengthening practice staff and services. But it remains unclear whether the DoH will sanction the move, with a spokeswoman warning that CCGs 'will not be able to commission primary medical services'.
The calls for CCGs to be able to top up primary care funding came as LMCs in England worked to strike local deals with PCTs to protect practice funding.
In Derbyshire, a deal agreed with practices could see some GMS practices give up part of their core funding to prevent cuts to other income streams.
Dr Gerada said the focus now must be on doing 'everything possible' to maintain community based, open access, independent general practice'.
She said CCGs should be able to use their budgets to increase GP numbers and improve GP services.
Dr Gerada admitted: 'CCGs are worrying about potential conflict of interest issues if they use their budgets to get more GPs doing more. But they shouldn't worry because it's the right thing to do.'
GPC deputy chairman Dr Richard Vautrey said CCGs could employ GPs directly or fund enhanced services deals to boost primary care.
'We would have no problems with CCGs employing GPs or providing additional resources for practices for them to employ GPs,' he said.
'But I am not sure it would solve the problem without that long-term commitment for practices to employ GPs.'
DoH national clinical commissioning network lead Dr James Kingsland said CCGs could use money released from service redesign to support capacity in general practice and primary care.
NHS Alliance chairman Dr Michael Dixon also said he could see no reason why CCG budgets should not be used to 'increase manpower in primary care'.
Efforts by Derbyshire LMC to protect practice funding and stave off cuts have seen practices in the county back a 'fairer funding' scheme that will adjust funding across PMS and GMS practices to a fixed rate of £78 per patient. A similar deal has been agreed in Liverpool.
Derbyshire LMC secretary Dr John Grenville said the deal would see funding for some PMS practices cut by 10% over four to five years.
Most GMS practices will gain from top-ups to funding under the deal, but a handful will give up part of their core pay, set by the nationally agreed GP contract, in a deal to prevent cuts to overall GP funding in the region.