The move was part of a government crackdown on the burgeoning commercial surrogacy industry and follows recent publicity over a Thai surrogate mother who said she was left with a baby rejected by his Australian biological parents after he was born with Down's syndrome.
The biological parents, who took the boy's healthy twin sister home, dispute the circumstances in which they abandoned their son.
Two Australian same-sex couples were prevented by Thai officials from leaving the Bangkok airport on Thursday with babies born to Thai women.
One couple had attempted to travel with the Thai surrogate mother in the hope of avoiding a challenge at the immigration desk.
Two US couples had also been prevented from leaving Thailand with babies since Wednesday.
Thai officials said the couples would have to apply for court orders to take the babies out of the country.