More than half of 147 tigers rescued three years ago have died, with 86 succumbing to illnesses.
The tigers were vulnerable to illness because of inbreeding, leading to laryngeal paralysis causing respiratory failure, according to national parks official Patarapol Maneeorn.
The DNA of all 147 confiscated tigers could be traced to six tigers who were the original breeding stock, said Dr Maneeorn, head of the department's Wildlife Health Management Division.
Such inbreeding "affects their well-being, resulting in disabilities and weakened health condition," he said at a news conference.
He added: "And when they have weakened genetic traits, they also have problems with their immune system as well."
The temple in the western province of Kanchanaburi served for more than a decade as a de facto zoo.
Tourists could feed tigers and pose for photos with them, despite concerns about possible mistreatment and suspicions of wildlife trafficking.
Police found tiger skins and teeth and at least 1,500 amulets made from tiger bones when they raided the temple.
There were also 60 cub carcasses stuffed in freezers and in formaldehyde in jars.
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Tiger parts, such as ground bones, are popular as traditional medicine in Asia. Tiger hides can sell for tens of thousands of dollars in China.
There are estimated to be more than 1,000 tigers in captivity in Thailand, but only about 200 in the wild out of a global wild population of about 4,000.
Dr Maneeorn said Thai authorities would do their best to care for the surviving rescued tigers.
"We are mobilising team members, increasing our readiness and adjusting our plan," he said. "We will provide the best care possible."
Additional reporting by agencies.