The discovery follows a scandal that erupted after an Australian couple were accused of abandoning a baby boy with Down syndrome born to a Thai surrogate, while taking home his twin sister.
There were no documents found with the nine babies, leading authorities at the emergency accommodation where they are being cared for to guess they are aged between two weeks and two years old.
A Thai lawyer who was at the apartment at the time of Wednesday's raid deepened the mystery by telling police that all nine babies were the children of an unnamed wealthy Japanese man.
Also present at the plush condominium in a city suburb were nine nannies and a pregnant woman, who later said she was acting as a surrogate mother. The nannies told authorities they were paid $310 a month to look after the children.
It was not immediately clear if the babies were also born to surrogate mothers.
"We're investigating how these nine babies came to be in that room," deputy national police chief Aek Angsananont told AFP.
"We have to prove who their parents are with DNA tests, and determine if they were born naturally or by surrogacy," he said, adding the probe would look at the legality of the surrogacies if any have taken place.
Police said it could take weeks to prove who their biological fathers and mothers are.
Thai authorities have stepped up their scrutiny of surrogacy in the kingdom, following the controversy involving the Australian couple who have denied they rejected the Down's baby - a seven-month-old named Gammy.
The Thai surrogate mother said she agreed to carry another Thai donor's egg fertilised by the Australian man in exchange for around $14,900.
The man, 56, has been exposed as a convicted paedophile in Australia.
Thai medical officials say surrogacy is illegal - unless it is with a relative - in the kingdom and offering money to carry a baby is outright prohibited.
"Surrogacy outside bloodline is illegal," Boonruang Triruangworawat, of the Public Health Ministry, told reporters Thursday.
There are 45 public and private surrogacy clinics in the kingdom and 240 doctors certified to carry out procedures.
"Currently clinic owners who allow (uncertified) doctors to perform surrogacy will be punished with one year in jail and a fine of $600."
But in the wake of the baby Gammy scandal, Thailand's new junta rulers have vowed to beef up punishments and close current loopholes which they say are being exploited by foreigners seeking Thai surrogates.
A draft bill proposes a tighter ban on commercial surrogacy carrying up to 10 years in jail for anyone - doctors, egg donors, prospective parents or surrogates - found in breach, according to a junta spokesman.