A message in red letters flashed up as Brisbane mum Lorraine Pacey applied for a childcare rebate and tried updating her marital status with Centrelink this week.
Ms Pacey, who married her wife in New Zealand in 2014, finally had her relationship recognised under Australian law when Parliament passed historic same-sex marriage legislation in December.
Centrelink's website told her otherwise when she tried changing her details on Monday while preparing to resume working after a year's maternity leave.
"You indicated that your relationship status is married and recorded your partner's sex as the same sex as yourself. Under Australian law, marriages between same-sex couples are not recognised," it said.
It asked her to "ensure" she selected the appropriate sex or relationship status.
"I was surprised at my emotional reaction to it," Ms Pacey said. "I took that message as being quite disrespectful and offensive."
On Facebook, friends and family reacted the same way.
"It just doesn't need to be that wording, in those big red letters," Ms Pacey said.
The department had only needed to replace the message with another saying the system was yet to be updated to reflect new legislation, she said.
The Department of Human Services, which runs Centrelink, said its online claiming systems were updated overnight to remove the message.
"We'd like to apologise to anybody who was distressed or offended by the message before it was removed," spokesman Hank Jongen said.
"Customers can be reassured that further work to update our systems to allow the department to record same-sex marriages is under way and we hope to have this rectified early next month.
"Unfortunately our current IT system houses layers of complex business rules and processes which means seemingly simple changes take time to work through to ensure they don't have unforeseen impacts on other parts of the system."
Mr Jongen said the department had recognised same-sex relationships for social security and family assistance purposes since July 2009.
Thousands of same-sex couples who married overseas had their vows recognised under Australian law in December after a majority of voters supported same-sex marriage and Parliament passed legislation.
Same-sex couples wedded around Australia on Tuesday, the first day they could legally marry without a waiver.
