It will enable PCTs to aggregate and compare the results of practices with similar patient populations across England for the first time.
This will include QOF performance, patient satisfaction and generic prescribing data in a 'traffic light' format.
However, GPs and practice managers fear the data could be flawed without detail about pounds-per-patient funding.
The tool is available to PCTs now and the NHS Information Centre will make it available to patients in January.
At the National Association of Primary Care (NAPC) conference in Birmingham last week, Jill Matthews, DoH national implementation director for primary care and community services, admitted that data quality might be an issue. But she said it should only suggest questions to managers, not dictate policy.
Ms Matthews said: 'If you have a practice manager making a strong case that their practice is different, you can ask this tool to find 40 practices with similar demographics.' She said the worst performing practices could learn from the best.
Practice manager Ray Guy, chairman of the North Liver-pool practice-based commissioning consortium, warned PCTs 'might use this as a stick to beat GPs with'.
He said practices receive between £50 and £200 per patient, and asked: 'Will this information take into account the variation in funding?'
Ms Matthews replied: 'We do not collect that nationally. But PCTs could put it in. It is actually fascinating how little correlation there is between investment and outcomes.'
Ms Matthews could not assure practices that managers interpreting the statistics would have received relevant training.