The 20-year-old Crest case management system, which runs ageing computers using an unsupported operating system, is long overdue for upgrade or replacement the report found.
"The lack of any facility for electronically transferring data into Crest leads to duplication and risks error, as staff have to re-key data," the report said.
But the report notes that HM Courts Service plans to address the risk of the Crest system by moving it on to modern and supported hardware and software by March 2011.
The report said the "replatforming" should facilitate functional improvements to be made to Crest in the future.
The report also criticised the Xhibit system designed to automatically update the court service's criminal justice partners on the outcome of cases through a web portal.
The system was introduced by the government to make it easier for the police, witnesses and the wider public to keep track of criminal cases.
Xhibit's slow speed and susceptibility to "crashing" at busy periods puts pressure on staff to maintain duplicate records, the report said.
The system has also not been updated since it was introduced in 2006 to reflect changes made to forms used to report the results of certain types of cases.
"For some cases staff are having to input data manually and either fax or post information to other service users," the report said.
HM Courts Service has put in place a programme to improve Xhibit's performance, but the report said it is too early to assess how successful this programme has been.
As of December 2008, HM Courts Service was also considering options for providing more flexible arrangements for updating the forms within Xhibit, the report said.