The tech failure forced the Australian Taxation Office to halt its online customer services from early afternoon until after 8pm, although its main webpage remained operational.

Taxpayers trying to lodge their tax returns were met with a webpage saying the service was temporarily unavailable.

A memo to staff confirmed the services would be out for several hours, as tax time began following the end of the financial year last week.

The outage came within hours of Tax Commissioner Chris Jordan appearing at Canberra's National Press Club, saying the annual tax season was under way without any system failures.

About 210,000 tax returns from individuals and agents have already been lodged online.

Mr Jordan told journalists he wished he could give an "iron-clad guarantee" that all online systems would work 100 per cent of the time.

"But that is not the reality when you are talking about very large and complex systems," he said.

"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," he said.

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

CPSU deputy secretary Melissa Donnelly likened the crash to the infamous ABS census debacle in 2016, saying the ATO was vulnerable because of a growing reliance on contractors.

"It simply isn't good enough that people and businesses can't complete their tax returns when demand is at such an entirely predictable peak," she said.

Australian Services Union official Jeff Lapidos said the IT crash was embarrassing for Mr Jordan given his comments at the National Press Club, but not surprising in light of the ATO's recent tech problems.

"The real worry is we don't know how long these outages will last for," he said.

The web shutdown comes after the ATO's website and internal systems crashed nine days before tax time and remained offline for several hours.

In a statement, the ATO said systems were restored before 9pm. It said no data has been lost and systems were not compromised or subject to a cyber-attack.

"We identified intermittent system issues early this afternoon affecting our mainframe and impacting on our services to the community. This was caused by applications running incorrectly.

"We took controlled action to reboot our mainframe and resolve this issue. We then brought our services back online methodically to ensure system availability and stability.

"While an outage is not optimal, our decision today to address our degraded system performance was to ensure they were fully operational for the 8.00-9.00pm window when we know the majority of people choose to lodge their tax returns."

In February the ATO could not guarantee it would begin tax time 2017 on July 1 as it scrambled desperately to save this year's tax return program from the fall-out of its disastrous pre-Christmas online meltdown.

The agency abandoned much of its IT program for 2017, and in the wake of the recent tech failures, peak tax accountancy body the Tax Institute said its members had lost confidence in the ATO's systems.

The revenue agency's online systems collapsed disastrously in mid-December, causing prolonged outages and again in February, even as technicians from the ATO and Hewlett Packard, the multinational tech giant which supplied the failed systems, continued to work on restoring capacity.

A report on the December and February outages released last month blamed multinational Hewlett Packard and stressed fibre optic cables for the chaos, saying technicians had failed to effectively respond to the escalating meltdown for nearly four hours.