At present, SCR is created on the basis of 'presumed consent', where patients will be included unless they opt out, but research has found most patients are not aware of the programme, raising questions about the system's ethics.
Carol Clarke, director for stakeholder engagement for the system, said that consent was 'fundamental'.
'We must go back to the drawing board,' she said.
She said Connecting for Health was looking at the system used in Scotland and Wales, where clinicians must get patients' consent before viewing their record.
But she warned that 'it's difficult to sit down every patient and ask their permission' before their records are uploaded.
A motion at this week's LMCs conference will call for no data to be added to the database 'without the patient's consent'.
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