The ATO said in a statement that the outage, reported as being longer than five hours by the ABC, was not connected to its ability to handle the filing of tax returns.
With the ending of the financial year 2016-17 on 30 June, Australians have to file their returns by 31 October. Since the online tax filing facility was made available by the ATO, the number of people filing returns has grown each year.
The ABC reported that the outage happened soon after tax commissioner Chris Jordan told the National Press Club that he was satisfied with the way ATO systems had been coping with the increased demand which is experienced at this time of the year.
"No data has been lost and our systems were not compromised or subject to a cyber attack," it said.
"We identified intermittent system issues early this (Wednesday) 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."
The ATO said Wednesday's outage had affected "ATO Online services (including myTax), The Tax Agent, Business and BAS Agent Portals, Standard Business Reporting (SBR), Australian Business Register (ABR) and our case management systems".
Jordan said during his address to the NPC that IT issues had had an adverse effect on the ATO's reputation.
"These outages were highly unusual and were disruptive for the users of our systems, particularly the tax profession, the superannuation and software industries," he said.
"I wish I could give you an ironclad guarantee that our systems would be available 100% 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."