Six-month-old Gammy has Down syndrome along with a congenital heart condition and a lung infection.
His surrogate mother, Pattharamon Chanbua, said Gammy was abandoned when his Australian parents took his sister home but left him. She said they had asked her to abort him.
A large and legally registered hospital located in a province near Bangkok provided the surrogacy service.
"We have found 12 surrogacy service clinics, only seven of which were legally registered with the HSS," said Ar-kom Praditsuwan, Director of the Department of Health Service Support (HSS).
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In Thailand, there are no specific laws regulating surrogacy services. Medical Council of Thailand regulations govern commercial surrogacy, which can proceed only if the egg and sperm come from a blood relative.
But Ar-kom said human trafficking or consumer protection laws may be examined if state authorities considered taking action.
Pattharamon declined to say where she had been taken to receive the surrogacy procedure. She said an Australian foundation will be responsible for the baby's treatment costs.