The National Audit Office found the General Practice Extraction Service had cost Â£40m to set up instead of Â£14m.
The system was meant to make data from GP systems in England available to bodies across the health service.
But the system has provided information to just one organisation - NHS England.
The NAO said in its current form, it was "unlikely" the system could deliver what it was set up for.
The idea was to create a system that could help gather information from GP surgeries, such as the number of patients being diagnosed with dementia or getting immunised, to help with research and monitoring.
It also provides information to determine how much doctors are paid.
As well as finding that GPES had run over budget, the National Audit Office also said it was delivered late.
The original plan was for the service to be up and running by 2010, but in the end it was not until April last year that data was sent to the first customer, NHS England, which has since used it a number of times.
However, no universities, academics or other organisations have been given data, mainly because of the time taken to extract it.
A spokeswoman for the Health and Social Care Information Service, which runs the system, said: "It is clear the procurement and design stage was not good enough."
She said the organisation was in the process of improving the system.
A new GP IT system designed to improve quality and planning in the NHS in England has been criticised for running over budget and behind schedule, by a finance watchdog.