A four-day Easter shutdown of much of the Tax office's online systems will make-or-break its ability to effectively stage Tax Time for millions of taxpayers this year.

ATO technicians will be working from Good Friday until Easter Monday to apply finishing touches and test the systems that have been installed to replace those that crashed disastrously in December and again in February.

Fairfax understands that Tax Office bosses will not be 100 per cent sure that Tax Time can go ahead as usual this year, until they get the results on Tuesday of the weekend's testing.

Much of the ATO's technical agenda for 2017 had to be abandoned as the agency struggled to recover from the disastrous crashes, and four key projects were prioritised with Tax Time identified as the number clear number one.

Commissioner of Taxation responded to Fairfax's coverage by saying he was "absolutely confident" the ATO will be able to receive and process tax returns on the traditional July 1 starting date. 

But much depends on the success or otherwise of the work being done this weekend with one source telling Fairfax that a successful weekend's work would all but assure Tax Time could go ahead as normal. 

But there would be "poo everywhere," if things did not go well over Easter, the source said.

The ATO's official message to tax agents and other users of its online service confirmed the Easter work was about getting ready for Tax Time.

"To provide resilient and stable systems for Tax Time 2017, we need to undertake additional weekend system maintenance in April and May," a public statement reads.

An ATO spokesperson would not answer questions on Wednesday about the consequences if this weekend's work goes badly.

"We are confident the new hardware will offer a better system for the future and enable us to provide the high quality experience and service the Australian community expects of us," she said in a statement.

The testing comes as the ATO faces more scrutiny of its online efforts with a parliamentary committee to inquire in the the Tax Office's defences against cyber-crime.  

The Joint Committee on Public Accounts and Audits has launched its inquiry after an Audit Office investigation raised concerns about cyber-security at the ATO and other large government departments.

"Cybersecurity is integral to protect government systems and secure the continued delivery of Government business," committee chairman Senator Dean Smith said.

The JCPAA also noted its concerns about the December and February outages of the ATO systems in the committee's review of the agency's annual report.

"The ongoing disruption to ATO online services over December 2016 and into 2017 brought into focus the potential risks associated with the digitisation of core government processing and support services, such as those managed by the tax, health and social security services," the committee's report noted. 

"While the ATO has given reassurance that no taxpayer data was lost during the outage, the Committee notes that concerns about the security of government held data exacerbates the effects on tax professionals and others in the community when core government processing and payment services, assistance and advice, goes offline."