Both the federal government's myGov website and Australian Taxation Office online services were down on Friday despite swelling numbers of taxpayers eager to lodge tax returns and receive the Coalition's boost to their refund.

The ATO blamed a technical problem with a communications switch for the outage that crippled its online services for clients, but said the glitch was unrelated to the myGov website failure.

Outages began in the morning and stretched into the afternoon, as for several hours the myGov fault blocked people trying to access payment summaries needed to lodge their tax returns.

Welfare recipients were also unable to report their employment income to Centrelink through the online hub for federal government services.

The Human Services Department, overseeing myGov, reported at 4.15pm it had restored the website progressively but warned a small amount of clients could still encounter intermittent problems as recovery work continued on Friday.

Department spokesman Hank Jongen said the disruption to the website, which started at 9.40am, did not stop regular overnight payments.

"We apologise for the inconvenience this outage undoubtedly caused for our customers. We understand the timing is unfortunate," he said.

Human Services extended the deadline for welfare recipients reporting their employment income to 7.30pm following delays caused by the IT failure.

The department flagged an investigation into the cause of the myGov website's outage but ruled out the possibility of a cyber attack.

The Tax Office denied an increased volume of website users caused its separate tech failure, which hit the agency in a week it began diverting staff from their regular work to cope with an unprecedented surge in calls about tax returns.

Changes to the payroll system left the ATO relying more on myGov for this year's tax-time, requiring taxpayers working for a business with more than 20 employees to retrieve their payment summary from the website.

More than one million people lodged a tax return in the first days of tax time this year after the Coalition's boost to refunds for low- and middle-income earners passed the Federal Parliament.

The Tax Office told clients on Friday morning online portals were down for taxpayers trying to lodge their returns.

Its online services remained down at 6pm.

The ATO said the glitch would have no impact on people who had already lodged returns, and paid 390,000 tax refunds with a value of $882 million into bank accounts on Friday morning.

It expected to pay another 110,000 refunds worth $292 million in the afternoon.

myGov, posting on Twitter earlier on Friday, said customers were unable to access Centrelink, Child Support and Medicare's online accounts and mobile apps.

Customers reported being unable to log in to deal with rejected Centrelink claims or receive information sent from the National Disability Insurance Agency through myGov.

Labor's Treasury spokesman Jim Chalmers described the outages as a shambles and a humiliation for the Coalition as it tried rolling out its tax offset.

"This is a government which told hundreds of thousands of Australians to get their tax return in, and then made it impossible for them to do so," he said.

Community and Public Sector Union deputy secretary Melissa Donnelly said the website outage was one in a long line of government IT failures.

"The community deserves more reliable digital government services and to achieve that we need better ICT investment and in-house capacity," she said.