The move was revealed as part of the chancellor's Autumn Statement.
Subject to analysis of costs, benefits and affordability issues, practice-level data on quantities of medicines prescribed will be published online by September 2012.
GPC deputy chairman Dr Richard Vautrey said the government would need to be careful about how information was used and released.
'What we want to avoid is league tables developing between different practices,' he said. 'We need to consider the added value that a practice offers to patients, because they may be working from very different starting points.'
He added: 'Any information has to be anonymised in such a way that it cannot indirectly draw attention to a particular patient or patient group.'
Dr Vautrey also pointed out that patient and government views of what makes a good practice may differ.
'In patients' minds, they often quite like practices that are willing to refer, and many patients would like to see more investment in expensive drugs,' he said.
