The Australian Taxation Office (ATO) has struggled to respond to a critical systems collapse this week.

The ATO's data storage systems crashed on Monday, knocking the agency's website, tax agent portal and case management system offline for several days.

The ATO’s primary and back-up storage systems crashed, corrupting data that then had to be restored from other back-up sources.

Systems are slowly being restored, but the problem has gone on long enough to attract some serious criticism.

“The real issue is how quickly it's all going to be back online and what that means for businesses that might have documents they needed to lodge, or payments they needed to make,” Paul Drum, the head of policy at CPA Australia, told the ABC.

CPA represents over 100,000 certified accountants.

“We need to make sure that when the system is back up and running, that the ATO is going to be cutting some slack to those businesses to ensure that they're not going to be fined for late lodgement or for late payment, as a consequence for the system failure at the ATO,” Mr Drum said.

The ATO says no data was lost.

“We will work with any client to ensure they are not disadvantaged as a result of the outage,” the agency said in a statement on its website.

“There has been no loss of data. No taxpayer information has been compromised.

“ATO experts and our partners at HPE [Hewlett Packard Enterprise] have continued to work around the clock to bring our core systems back online.”

Mr Drum said the outage does not help the public’s perception of the government’s competence in data management.

“It's certainly embarrassing for the ATO, but I also think it's embarrassing on a broader level,” he said.

“Not long ago we had the issue with the census and IBM, and the Government lost face over that.

“I think some will be making a call on the Government to say; ‘Are they resourcing the tax office properly to enable it to do its job?’.

“Our members rely on these systems and the ATO to be able to do their job and provide services to their clients, and at the moment their hands are tied.”

The ATO says full services should be back in a few days.

“We are working towards bringing the Tax Agent Portal back online later today,” a spokesperson said.

“After full restoration, investigations will continue on the cause of the outage to ensure we treat the underlying issue.”