Hundreds of inaccurate patient records have been created every day because of a fault on the new NHS computer system.
MPs say the IT programme is behind schedule
The problem - affecting patients in Greater Manchester with appointments booked via the online system - arose after a software upgrade.
NHS Connecting for Health, which is overseeing the IT upgrade, said the fault would not affect patient care.
The nationwide programme has been hit by problems and has been criticised by MPs, who warned it could cost £12.4bn.
A spokesman for NHS Connecting for Health said the problem was expected to be fixed in the next few weeks.
He said: "Although comprehensive testing is undertaken prior to the upgrades taking place, it is not unusual for these kinds of upgrades to identify teething problems in the early stages following implementation.
"We estimate that around 400 duplicate patient records might have been created each day.
"However, the system is being continually monitored throughout each day and where a duplicate is identified data is being merged to form one single record for each patient."
Before the fault is fixed permanently, an interim solution has been put in place to identify the duplicate records and correct them, the spokesman added.
"This has now been put in place with the full agreement of those organisations affected and will have minimal impact on the users of the system and no impact on the delivery of patient care," he said.
Among the places affected by the problem are the University Hospital of South Manchester Foundation Trust and PCT Clinical Assessment Centres in Greater Manchester.
The upgrade of the NHS IT programme is set to link more than 30,000 GPs in England to nearly 300 hospitals by 2014, and includes an electronic medical records system and e-prescriptions.
A committee of MPs recently warned that delays and costs of the multi-billion pound NHS information technology upgrade meant its future "did not look good".
Medics have also raised concerns over patient confidentiality because records will be accessible all over the country.