A spokesman for Bangkok's Central Juvenile Court said: "For the happiness and opportunities which the 13 children will receive from their biological father, who does not have a history of bad behaviour, the court rules that all 13 born from surrogacy to be legal children of the plaintiff".
"I've never seen a case like this", the Thailand director of Interpol said about what the country dubbed the "baby factory", after tips led the worldwide policing group to investigate amid concerns of human trafficking.
Shigeta hired the Thai surrogates before the ban on foreigners.
All 13 babies linked to Shigeta in Thailand have since been put under the care of the ministry's shelters for children, while Shigeta himself has assigned representatives to regularly visit his children. Mariam Kukunashvili, founder of the global clinic, told the Associated Press in 2014 that Shigeta submitted requests for new mothers soon after others became pregnant.
The court said it did not find evidence of human trafficking.
"He said he wanted 10 to 15 babies a year, and that he wanted to continue the baby-making process until he's dead", she said, adding that he asked about equipment to preserve sperm in old age.
Shigeta, who allegedly wanted to start a "big family", has been providing the children English and Japanese tuition while they've been in government care these past few years.
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It was widely speculated that the woman might have turned against him after finding out he was gay. Shigeta was identified as the father.
He also has two children via surrogates in India, CNN reported. The 28-year-old was not present in court when the verdict was announced, the Bangkok Post reported.
"The case of Mitsutoki Shigeta is way outside the norm for cross-border surrogacy", Everingham said.
Shigeta, the son of a Japanese tycoon, left the country in the wake of the scandal but later took Thailand's Ministry of Social Development and Human Security to court for custody of the children. Police at the time said that Shigeta paid the surrogates between $9,300 and 12,500 each to carry his children.
Mitsutoki Shigeta, the scion of a Japanese telecom billionaire, fled Thailand soon after a police raid on a Lat Phrao condo discovered many babies stored there.
According to Tuesday's court statement, Shigeta has taken care of other children, born from surrogacy, and raised them in Japan and Cambodia, where they were well looked after.
The court gave no further details about the man, but said he plans to raise the 13 children, all aged about four, in Japan where he lives, adding that he had previously raised other surrogate children in Cambodia and Japan.