The Independent Safeguarding Authority (ISA) vetting and barring scheme has been developed in response to the Soham murders.
The scheme requires anyone who could have access to records and personal information relating to potentially vulnerable individuals to be checked at a cost of £64 per person.
This means that anyone working in a practice will require checking regardless of their role.
It will also be a requirement for anyone who applies for a post in general practice to be registered with the ISA.
The scheme begins in October but the Home Office announced in March that registration of individuals would not start until July 2010.
Employers cannot begin to check potential employees until November next year.
Jon Ford, head of the BMA health policy and economic research unit, said the costs involved in running checks could exceed £7.5 million for general practice.
The cost to each practice would be about £960, depending on the number of people it employed.
'There are about 8,000 practices and about 120,000 practice staff in terms of a head count. That's about 15 people per practice,' said Mr Ford.
The initiative is to run in conjunction with the current Criminal Records Bureau system in England, Wales and Northern Ireland.
The scheme was developed in response to the Bichard Inquiry report into the murders of Jessica Chapman and Holly Wells by school caretaker Ian Huntley.
It aims to ensure that those who are known to present a risk of harm to others are prevented from entering the workforce.
It is a step forward from the existing Protection of Vulnerable Adults (PoVA) scheme, which was implemented in social care settings but did not apply to the NHS.
NHS Employers is to run four roadshows in June and July on the new system in Leeds, Birmingham, London and Bristol.
Cost of ISA checks
- £64 per member of staff.
- 15 members of staff in an average practice.
- £960 is the total cost of checks per practice.
- £7.5 million is the cost to English general practice.