NHS England requires all CCGs to involve 'at least one secondary care specialist and a nurse' on their governing body.
But a BMA poll of 284 consultants found that one in 10 said there were no secondary care clinicians on their local CCG board.
The BMA has called for more transparency in how secondary doctors are appointed to CCG boards because the groups are not allowed to appoint a clinician employed by any organisation they commission from.
BMA consultants committee joint deputy chairman Dr Tom Kane said: ‘We predicted this would cause significant difficulties. It has been unclear how CCGs have been making these appointments and the survey only reinforces these concerns.
‘There was a need for CCGs to make greater efforts to seek applicants openly.’
The survey revealed that 70% of consultants were unaware of how secondary care doctors were recruited to CCGs and seven in 10 were unaware which type of doctor was on their CCG board.
GP leaders have previously called for stronger safeguards against conflicts of interest in clinical commissioning after an investigation revealed more than a third of GPs on CCG boards have links to private providers.
GPC chairman Dr Chaand Nagpaul said: ‘It is important for GPs and consultants to work collaboratively to develop clinical pathways and maximise and improve patient care’.
An NHS England spokeswoman said: ‘A number of measures were introduced to ensure the voices of clinicians other than GPs were heard more clearly in the commissioning process.
‘This included membership of at least one secondary care specialist and a nurse on the governing body.
‘To address concerns about conflict of interest that secondary care specialist must not be an employee or a member, or a partner, in a provider of primary medical services or a body from whom the CCG commissions services. All 211 CCGs should have a secondary care doctor on board.’