The two girls were pulled off the flight and stayed at the Novotel Hotel at Brisbane Airport overnight, she said.
They were due to leave on another flight to Italy about 8pm local time last night.
The aunt says the Queensland Department of Child Safety did not tell the family that the two girls weren't on the flight.
The four sisters, aged nine to 15, were forcibly removed from their Sunshine Coast home on Wednesday night by Australian Federal Police after a Brisbane judge on Wednesday dismissed the mother's last-ditch application to keep them in Australia.
Seven Network footage shows the girls screaming "no" and resisting before they are put in two cars.
Their mother banged on the rear window of one vehicle as it drove off.
She ran after the car and then collapsed to the ground sobbing.
The sisters were driven to the Brisbane Airport and taken to the boarding gate by the officers as one girl wailed, "Let me go. I want my mum, I want my mum."
Their mother watched on, telling them "I love you".
"I'm just praying, I'm just praying. I don't know what to think. I'm terrified right now."
Brisbane Family Court Justice Colin Forrest ruled on Wednesday that the girls were wrongfully kept in Australia and there were insufficient exceptional circumstances to allow them to stay.
However, he refused to make the order to return the children to Italy until their father gave an undertaking to withdraw any criminal complaint against their mother.
The girls' aunt, who acted as the litigation guardian during the case, said the mother had told her she wouldn't return to Italy to be with the girls.
She is a student and has no money.
"She has absolutely no money, none of us do, so we can't support her financially in Italy, either," the aunt told AAP.
The family also fears the mother would be prosecuted and victimised despite the father's assurance to the Family Court.
"I know that the courts have got an undertaking from the father that he won't prosecute her in any way in Italy, but I'm not sure that holds any weight once he's in another country," she said.
"We're certainly sceptical on whether there would be any consequence for not holding him to that undertaking.
"It's the only reason (she's not going back). What good is she to her daughters if she's in prison?
"Going to Italy and being completely isolated from her daughters and risking her being imprisoned, it makes no sense."
The great aunt also said the girls' father had turned his village against the mother.
"I would say she would be unwelcome," she said.
The sisters attracted international media attention in May when they went into hiding to avoid a 2011 Family Court order to return to Italy, where they are the subject of a custody dispute.
The sisters, who hold dual Italian and Australian citizenship, travelled to Australia with their mother in 2010 for a one-month holiday and did not return.
A further custody case will now be dealt with in Italy.
The Department of Child Safety wouldn't confirm the location of the sisters or that two had been pulled off the flight.
A spokeswoman would only say the department would help enforce the order.
"We're working with the Australian Federal Police to make arrangements to comply with the order of the Family Court made under the Hague Convention," the spokeswoman told AAP.
- AAP
