The tax office says users of its online systems can expect disruptions as it seeks to fix problems which emerged late last year.
A business reporting system known as SBR1 failed last Friday but was resolved that afternoon, AAP has been told.
An Australian Taxation Office spokeswoman described the event as a "minor disruption".
"The complexity of the restoration means there is still work being done to return our services to normal. There may be some disruptions to service as this work is undertaken," the spokeswoman told AAP on Thursday.
"Information about our systems continues to be updated on the website and through our social media channels."
The ATO took its systems offline to conduct a "critical system maintenance" last weekend as the agency sought to restore systems to full functionality.
It also undertook a significant amount of work over the Christmas break to ensure its website and portals are functioning properly.
Commissioner of Taxation Chris Jordan described last year's event as the "worst unplanned system outage in recent memory".
It was caused by an unprecedented failure of storage hardware, which had been upgraded in November 2015 by Hewlett Packard Enterprise.
What compounded the problem beyond the initial failure was the subsequent failure of the ATO's back-up arrangements to work as planned.
However, there was no loss or compromise of data and refunds had been fast-tracked.
The ATO has ordered an independent review to find out what happened, how and why, and what measures need to be taken to avoid such a situation in the future.
