Mainframe problems forced the Australian Taxation Office to take most of its online portals and internal processing systems down for maintenance for the back half of Wednesday, during the first week of 2017 tax time.

Customers began complaining about an inability to access the ATO's myTax system through the myGov portal around lunchtime on Wednesday. Some reported receiving an "A951.09" error when trying to access the page.

The issues emerged at the same time ATO commissioner Chris Jordan was giving a speech to the National Press Club on the performance of the agency's systems so far in this year's peak tax period.

The ATO told taxpayers it would need to take its portals, myTax, and other online services offline on Wednesday afternoon to "resolve some intermittent system issues".

An internal message to staff, sighted by iTnews, revealed most of its internal processing systems were also impacted, and warned the outage could last "a few hours".

At 8:30pm the ATO advised that its systems were again operational.

It blamed the problem on "applications running incorrectly".

"We took controlled action to reboot our mainframe and resolve this issue," it said in a statement.

"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."

It has been a struggle for the agency to move past the ongoing issues stemming from the collapse of its HPE 3PAR storage area network (SAN) last December and February this year.

Late last month it suffered an unrelated but similar storage failure with its other main IT contractor Leidos.

Jordan told the press club the agency had so far received 210,000 returns "without a hitch" for tax time 2017, prior to today's issues.

"I wish I could give an iron-clad guarantee that all systems will work 100 percent of the time. But that is not reality when you are talking about very large and complex systems," he said.

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

An independent analysis - prompted by the HPE storage collapse - of the ATO's entire IT environment is currently underway, intended to "identify and reduce the risks of future unplanned outages", Jordan said.

"We are well aware that if we are to offer and encourage the use of digital services, then we have to have our systems available when people need them."