A computer glitch is being blamed after 73,000 families who are paid family tax benefit were told they were due to pay back up to $800 each.

Centrelink has said sorry to its customers, the second mass apology the agency has had to issue in recent months.

In November and December, clients suffered through weeks of disruption to the Centrelink websites used by millions of Australians to manage their payments and report their work activities.

The agency was forced to apologise after weeks of "intermittent issues" left many clients unable to log on to their accounts.

The department was savaged in a mid-year National Audit Office report for its customer service performance and and Fairfax revealed last month that the Commonwealth Ombudsman was fielding complaints about Centrelink at an average rate of 660 a month.

Centrelink's tech troubles have also hit efforts to crack down on dodgy disability benefits claims with doctors unable to lodge their reports on the agency's malfunctioning web portal.

A centrelink spokeswoman said on Thursday that the false debts raised with the family tax benefit clients had been fixed and nobody had been left out of pocket.

"We are aware a small proportion of Family Tax Benefit customers, 73,000 or less than 5 per cent of total FTB customers, temporarily had an incorrect debt displaying in their online accounts or the Express Plus app," she said.

"This incorrect debt display has now been fixed and is no longer showing in customer's accounts.

"We apologise for any inconvenience and can reassure this did not have any financial impact on customers. "