Health secretary Patricia Hewitt announced this week that the medical training application service (MTAS) will no longer be used to recruit junior doctors.
After the first round of recruitment, applications for specialist training posts will now be overseen locally by medical deaneries.
British Medical Association junior doctors committee vice chair Dr Andrew Rowland welcomed the demise of the 'unfair, discredited, and shambolic MTAS system'.
Ms Hewitt also referred to last month's error, when applicants' personal details could be seen by the public on the online system.
Police are handling the case after an investigation revealed there had been two security breaches and criminal offences may have been committed.
The decision follows growing criticism of the system and the announcement by junior doctors' organisation Remedy UK that they are taking the Department of Health to court.
The planned two-day judicial review, due to conclude today, will decide whether the system should be ditched altogether, including the first round of recruitment.