The advice follows reports that the government is considering cutting back protection of public-sector pensions to encourage private firms to bid for more public services.
The Treasury launched a consultation last week on guidelines that protect public sector pensions.
Dr Andrew Dearden, chairman of the BMA's pensions committee, warned removing protection for NHS staff whose jobs move to private firms or social enterprises would be a 'blatant attempt to prepare the NHS for privatisation'.
GPC deputy chairman Dr Richard Vautrey said young GPs need to increasingly look at pensions schemes early in their careers.
He said young GPs looking to work for private companies must scrutinise the pension arrangements offered.
'I would urge young doctors to look carefully at the contract they are entering and ensure they are getting what they deserve,' he said.
He added that young GPs taking a tough stance on pensions could help prevent private firms moving rapidly into providing NHS services.
Chairman of the Conservative Medical Society Dr Paul Charlson warned that any attempt to erode GP pensions could undermine morale as the profession takes on commissioning responsibility.
Meanwhile, Dr Charlson said the government has to handle any pension renegotiations 'incredibly carefully' to ensure that it does not alienate GPs in any way.
He said any intention to interfere with GP pensions will 'not go down well' with the profession.
'The government will be reliant on GPs to make these commissioning changes, and it will only work if GPs are generally supportive,' he said.
'If there are too many things that upset GPs it's going to make them more reluctant to move changes forward.'