The Australian Taxation Office said it cannot guarantee that its website will remain free from outages after an IT issue forced the system offline for more than five hours.
The ATO said full functionality has been restored to its systems, after an outage on Wednesday afternoon.
The ATO's acting chief operating officer Francis Cawthra said with such heavy demand on the system during this peak period for tax returns, no guarantee can be made that the system will remain online.
"These are very large, they're very complex systems you know in today's world," she told the ABC. "And it's just not a guarantee we can give. We do have every confidence that we are well on a way to a very good tax time."
Defending its handling of the incident, the ATO said the outage was not related to its capability to deliver during the peak tax return period.
ATO portals, myTax and other online services went down on Wednesday afternoon as staff attempted to resolve "some intermittent system issues".
The ABC reported the outage began during Wednesday's National Press Club address delivered by tax commissioner Chris Jordan.
The outage reportedly began when he was telling the audence that he was satisfied with the way ATO systems had been coping with the increased demand during the peak tax return period.
The website has been dogged by system issues in recent months, with major outages in December, February and as recently as last week.
The office on Wednesday night released a statement to "set the story straight" and defend its handling of the incident.
The statement admitted an outage was "not optimal", but the decision to pull services offline was made to make sure systems were fully operational for a peak traffic window of 8pm to 9pm.
The problems were not related to recent hardware issues and no data had been lost, it said, nor were the systems 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," the ATO said in a statement.
"This was caused by applications running incorrectly."
A reboot of the mainframe fixed the problem.
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