The Government Gateway, which allows citizens and businesses to carry out secure transactions on government IT systems, was shut down last Monday to minimise the risk to personnel and infrastructure following a fire that broke out at a contractor's datacentre.
The decision was made even though September is one of the busiest periods for the Revenue with taxpayers rushing to submit self-assessment forms before the end of the month.
The Revenue told CW360: "People could fill in their forms online but they could not send them. We have a contingency plan in which online tax-filing can revert back to the Inland Revenue Web site if there is a problem with the Gateway but it was thought that this was not a big enough problem for that to be necessary."
Chas Roy-Chowdhury, head of taxation at the Association of Chartered Certified Accountants (ACCA), said: "The Inland Revenue's online filing system already lacks credibility and this incident just makes things worse. This is one of the peak times for people wanting to file tax returns and the Revenue must get its finger out. Anyone who tried but was unable to file online during the 36 hours that the Gateway was shut down may never go back to online filing again."
A major report by the ACCA earlier this year highlighted persistent problems with the Revenue's online filing system, including delays in processing returns and some returns going missing altogether.
Even e-envoy Andrew Pinder has described online tax returns as a failure so far after the Revenue admitted less than 50,000 taxpayers used the service in its first troubled year.