The Australian Taxation Office's online services were taken offline for more than five hours on Wednesday, frustrating thousands of Australians hoping to lodge their tax returns.

Key points: Online service to lodge tax returns was offline for more than five hours

Online service to lodge tax returns was offline for more than five hours Outage not caused by a denial of service attack or a cyber-attack

Outage not caused by a denial of service attack or a cyber-attack Tax commissioner had said ATO has "ground to make up" on reputation and credibility

The system outage came just hours after tax commissioner Chris Jordan said he was pleased with how the IT systems had been handling the increased traffic during tax time.

The outage was not caused by a denial of service attack or a cyber-attack and a spokesman for the office says no data was lost or compromised.

"We identified intermittent system issues early this afternoon [on Wednesday] affecting our mainframe and impacting on our services to the community," said an ATO statement.

"This was caused by applications running incorrectly. We took controlled action to reboot our mainframe and resolve this issue."

The decision to take services offline was designed to ensure the online services were available between 8pm and 9pm, which is when most Australians lodge their tax returns.

People visiting the ATO website see a notice saying the service is unavailable.

The tax office has apologised for any inconvenience.

Earlier on Wednesday, tax commissioner Chris Jordan told the National Press Club IT issues were damaging the ATO's reputation and credibility.

"There is no getting away from the fact that these … matters have had a negative impact on the ATO's standing in the community," he said.

"I understand only too well we have ground to make up."

The tax office has struggled with multiple unplanned IT outages as recently as December, February and late June.

"These outages were highly unusual and were disruptive for the users of our systems, particularly the tax profession, the superannuation and software industries," Mr Jordan said.

"I wish I could give you an ironclad guarantee that our systems would be available 100 per cent of the time.

"That is simply not reality when you are talking about very large and complex systems.

"While we believe we have done everything we can and expect things to go smoothly, we are ready to respond quickly if there are any hiccups or unexpected outages."