The Inland Revenue has been forced to send out e-mails to the 110,000 taxpayers who registered to file online, urging them to try the service again.
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"If you resorted to sending a paper return this year please don't be put off. Come back and try our new, improved Internet service next time," the Revenue pleaded.
Online filing is a key part of the Revenue's drive towards e-business, but its system has been dogged by technical difficulties, with would-be online taxpayers reporting their returns being rejected for trivial mistakes.
In another development of its IT programme, the Revenue has decided to roll out its i2k desktop infrastructure into former Contributions Agency areas.
The Revenue has had difficulty linking its systems with those of the former Contributions Agency, including the Nirs2 National Insurance records system.
EDS and Accenture (formerly Andersen Consulting) are co-operating on the project, which will be piloted at five sites, although staff there may question the extent to which the systems are integrated.
"The pilot will provide people with both i2k and DSS desktops. This means that each user will have two PC base units with one monitor and a switch so they can change access between i2k and the DSS infrastructure," the Revenue said.