Under the agency's proposals, all patients in England will have a detailed record held locally where they receive treatment, and a summary record on the database.
These summaries will be extracted from local records held by GP practices once they are accredited for high-quality record-keeping under the IT directed enhanced service announced in December.
The IT agency believes the initial data upload to create the summary records should happen automatically unless patients opt out. A campaign is planned to publicise this approach.
However, the GPC voted last week to 'insist that clinical data should not be uploaded to the summary record without the valid informed consent'.
In effect, patients would have to opt in to having their records on the database, rather than opt out.
A report given to GPC members prior to the vote says: 'GPs who seek the opt-in model are not attempting to block the sharing of patient information, they are simply suggesting that the patient ought to be asked first and given the choice of how and when their information is used.'
The report adds that the opt-in model is backed by the RCGP's ethics committee, its IT group, and by the joint GP IT committee that encompasses RCGP and GPC IT committee members.
The public also back the opt-in model overwhelmingly, according to surveys by YouGov and the NHS Information Authority.
GPC chairman Dr Hamish Meldrum said: 'The summary information covers key diagnoses, demographics and drug information, but maybe not sensitive information about mental health and STIs for example.
'But what is non-sensitive can vary. A patient's summary could list a cocktail of drugs to treat HIV - that is clearly sensitive.'
He recognised that there were arguments in favour of the automatic upload and called for a wide public discussion, including a debate in parliament.
A spokesman for Connecting for Health said the opt-out model had been adopted only after substantial public research.
'We recognise there is an ongoing debate on the issue,' he said.
WHAT GPC WANTS
Patients must give informed consent that clinical data held by practices can be uploaded to their summary record on the national database.