Last week outages hit the agency's IT systems, forcing some tax return websites offline at short notice and leaving users unable to lodge information.

The failure, which came after a horror few months for the Tax Office, was caused by applications running incorrectly and requiring an immediate reboot.

In a statement released on Wednesday, officials sought to talk up stability and certainty in ATO systems, but acknowledged more disruption could take place in the future.

After conceding the third major outage since December would damage public trust in the agency, the statement said regular meltdowns were impacting tax and superannuation agents, digital service providers and businesses.

The issues were related to hardware and mainframes as well as human error and have prompted a review.

"The issues we have encountered with our systems over the past few weeks highlight the sheer size, scale, and complexity of the ATO's IT environment," the statement said.

"We continue to examine the triggers and cause of these issues and this analysis is informing the ongoing remediation work we are undertaking.

"While we are doing everything we can to minimise the risk of being exposed to systems incidents in the future and the resulting impact these incidents have on our stakeholders, we do anticipate there may be some further minimal disruption to our services as we continue work to implement the IT improvements identified in the report."

The statement said tax agents and individuals would not face penalties for failing to lodge or lodging late 2015-16 income tax returns. The ATO will automatically refund or not impose the penalties for lodgements due from December, provided they are lodged by August 31 this year.

So far more than 700,000 tax lodgements have been received from the 2017 return season and more than $500 million in returns processed.

"Results from tax time 2017 give us confidence that we are on the right track and in large part, the systems are working as expected," the statement said.

Seniorcounsel at the Tax Institute, Robert Deutsch, welcomed the August 31 deadline.

"The ATO has quite properly recognised the impact the recent ongoing outages is having both on their own IT systems and on the myriad of hard working tax agents and practitioners who are just trying to do their job to assist taxpayers to meet their tax obligations.

"The effective time extension to that date for statements and returns due to be lodged from December 2016 is quite generous but may need further extension if there are any further outages before August 31," Professor Deutsch said.

"The change does not however affect the due date for payment of the relevant tax; it is only the form that can be lodged late. The payment must still be made on time".

Last week the ATO's acting chief operations officer, Frances Cawthra, said the failures could have been worse if officials hadn't acted quickly and said no data had been lost.

The outage came hours after Tax Commissioner Chris Jordan told journalists the tax season was under way without any system failures.

Multinational Hewlett Packard was blamed for crashes of internal storage networks in December and February, causing much of the agency's work to slow to a halt and scores of staff to be sent home.

The ATO is dealing with fall out from the $165 million Plutus tax scandal as well as reports a staffer had to be disciplined for publishing a step-by-step guide to hack mobile phones on a social networking website.