The man, who cannot be identified for legal reasons, was charged in a New South Wales state court last year with committing acts of indecency with a victim under 10 years old, court documents showed today.
The girls were around 4 and 5 years old, Nine Network television reported.
The charges are the latest blow to the credibility to the commercial surrogacy industry in Thailand, which the Southeast Asian country's military junta has vowed to shut down.
The man, who denies the allegations, will go to trial in the New South Wales District Court in the coastal city of Gosford, 75 kilometres (45 miles) north of Sydney on December 8, documents showed. He is currently free on bail.
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The twins were born about seven years ago to a 23-year-old Thai surrogate mother, Siriwan Nitichad, also known as Aon, who lives in the Petchabun province, 400 kilometres (250 miles) north of Bangkok.
The man was then aged in his 40s and his wife was older, Nine reported.
"They said they were just married and they really wanted to have a baby so much," Aon told ABC. "She said her husband wanted to have a baby so much, please help them, please help them."
Aon agreed to use her own eggs with the Australian man's sperm. Aon said she was paid USD 5,300.
She said the twins were born with lung and other health problems. They were four or five months old before she handed them over to the Australians.
"If they asked if they could cancel their payment and we kept the babies, I would definitely have said 'yes,'" she added.
Court documents reveal the father became unemployed, allegedly had a violent temper, and the marriage broke down, ABC reported.
The children are now in the care of the ex-wife of the accused man, and Australian child welfare authorities are working on plans for their care, ABC reported.