Last week, Computer Weekly revealed that pay and tax details went missing as the Revenue sought to transfer records from Andersen Consulting's National Insurance Recording System (Nirs2) to the much older Computerised Operation of PAYE (Cop) system run by EDS under a 10-year outsourcing contract.
A high-level internal Revenue memo leaked to Computer Weekly had revealed that an investigation had begun to try and locate up to 5.2 million tax records for 1998/99 that Cop was expecting to receive but, for legitimate reasons or otherwise, had apparently gone missing.
But the Revenue published a statement on its Web site that said the "suggestion that millions of tax records have gone missing is wrong". The statement went on to deny that "there is any problem with the systems".
However, the memo refers to "missing 1998/99 pay and tax details", difficulties with optical character recognition and problems with an interface between Nirs2 and Cop.
After Computer Weekly made the memo available to the media, its contents were reported on national television and radio as well as on the front pages of The Times and The Guardian.
This week the Revenue denied it was "about hiding or denying any facts". It said the issue is "about fully reconciling data held on two large and complex IT systems".