Mitsutoki Shigeta, 28, became the centre of a "baby factory" scandal in 2014 after Thai police found a plush Bangkok apartment packed with infants under the care of 24-hour nannies.
A probe later found he had fathered 19 children in total, 13 surrogate babies living in Thailand and six others living in Cambodia and Japan, according to an official from Thailand's Social Development and Welfare Department.
Four of the six children living in Cambodia and Japan were from Thai surrogates.
Shigeta's bizarre case threw a spotlight on the kingdom's unregulated rent-a-womb industry, prompting authorities to bar foreigners in 2015 from paying for Thai surrogates.
Shigeta, reportedly the son of a Japanese IT tycoon, left the country in the wake of the scandal and has never directly explained why he fathered so many children.
But he later took Thailand's Ministry of Social Development and Human Security to court to seek custody of the children.
On Tuesday a Bangkok court granted him legal rights to take the children, saying he had ample money to care for them and had prepared nurses and nannies at a safe residence in Japan.
"For the happiness and opportunities the 13 children will receive from their biological father -- who does not have a history of bad behaviour -- the court rules them to be the plaintiff's legal children," the Central Juvenile Court said in a statement which did not mention Shigeta by name for privacy reasons.
Shigeta, who did not attend the trial, was deemed "sole parent" of the children after the Thai surrogates had signed away their rights, the court added.
His lawyer Kong Suriyamontol said he would contact Thai authorities about the next steps to transfer the children from state custody, adding that the timeline would depend on the "readiness" of the youngsters -- most of whom are aged around four.
Thai officials had visited Shigeta's homes in Japan as well as in Cambodia and deemed the children would be able to adapt to new surroundings.
Shigeta's mother has also been visiting the children in Thailand and "they have got used to her", he added.
Shigeta hired the Thai surrogates before the ban on foreigners. Police said he paid them between $9,300 and $12,500 each.
Thailand's rewriting of its surrogacy laws sparked a series of legal tussles, including a 14-month custody war between a same-sex couple and a Thai surrogate who was eventually forced to give up the baby girl.
Another high-profile case saw a Thai surrogate lose a court battle to bring back a baby after learning the Australian father was a convicted paedophile.
Sam Everingham, director of the Australia-based consultancy Families Through Surrogacy, said Shigeta's case was an "abuse of surrogacy" services that had helped give the controversial industry a bad name.
After Thailand clamped down on the trade surrogacy agencies quickly migrated to neighbouring Cambodia, which followed suit and barred the industry in 2016.
In recent months there have been signs the business is growing in Laos, an opaque communist country with no restrictions on surrogacy.
Some surrogacy agencies are now offering to carry out the embryo transfer in Laos and then provide pregnancy care for the surrogate in Thailand, a wealthier country with vastly superior medical facilities.
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