Australia has sought assistance from Thailand to enable a "transition period" for Australians with children, including the unborn, of Thai surrogate mothers to complete the process and enable them to leave for Australia.
The moves follows Thai immigration officials preventing two Australian couples from departing the country with surrogate babies in recent days.
Australian media reports said the same-sex couples, including one travelling with the surrogate mother, were prevented from leaving Thailand on Thursday.
A senior Thai foreign ministry official has confirmed the reports, saying further background checks were being carried out on the couples.
The Australian Department of Foreign Affairs and Trade said in a statement that embassy officials in Bangkok were "assisting Australians with children born by surrogacy in Thailand who have been prevented from departing the country in recent days".
It said Thai authorities were now "enforcing strict documentation requirements upon exit of the country when they
suspect a child has been born by surrogacy in Thailand".
Thailand's crackdown on surrogacy
Under the new measures, couples will require permission from the Thai Family Juvenile Court to be cleared to take babies born to Thai surrogate mothers out of the country.
The department said while regulation of surrogacy in Thailand was a matter for Thai authorities, Australia was continuing "to encourage Thai authorities to adopt appropriate transitional arrangements for any new measures they may introduce, so concerned Australians are not unduly affected".
The warnings come as Thai authorities pressed on with investigations as police and health officials raided and shut down an obstetrics and gynecological clinic in central Bangkok.
Thai police allege the clinic, New Life IVF clinic, was linked to the discovery of nine babies reportedly fathered by Japanese businessman Mitsutoki Shigeta, who may have fathered a further six children.
The expose covering Shigeta followed claims from 21-year-old Thai woman Pattaramon Chanbua, the surrogate for a West Australian couple's twins.
She alleges the couple took a healthy baby girl, but abandoned her twin brother, known as baby Gammy, after being told he had Down's syndrome.
The case and media attention highlighted lapses in Thai laws covering commercial surrogacy, triggering the Thai military government to speed up the process of implementing draft laws.
The laws tighten and clarify surrogacy but effectively ban commercial surrogacy, prohibiting advertising and brokers.
Australians happy to flout surrogacy laws
This comes as new research reveals Australians are far more likely to look overseas for a surrogate mother and enter into a commercial surrogacy arrangement, despite it often being in breach of Australian state laws.
The study by Jean Hailes Research Unit at Monash University and Surrogacy Australia was published in the Medical Journal of Australia. It found only 8 per cent of couples surveyed found domestic surrogacy arrangements.
"Of the people we surveyed most considered and actually went overseas to do surrogacy in spite of laws that actually prohibit people from going overseas to do surrogacy - and in spite of a lot of people wishing to do it in Australia," says Dr Karin Hammarberg who co-authored the report.
Dr Hammarberg believes the strict regulations around surrogacy arrangements - particularly rules which prevent money passing hands and the advertising for a potential surrogate - make it difficult for couples to find willing surrogates within Australia.
She thinks the Australians who were considering Thailand for surrogacy would be unwilling to place themselves in the position of those currently caught up in the country's crackdown.
"I can't begin to imagine especially if you are in the process and perhaps halfway through a pregnancy or you've just got embryos ready to be transferred to a surrogate. I think it must be extremely distressing for everyone," she says.
