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Wildlife authorities swooped on the Buddhist temple in Kanchanaburi near Bangkok on Monday under international pressure over suspected trafficking and abuse.
While animals were being sedated and removed from the centre on Wednesday, the bodies of 40 cubs were found in a freezer.
The freezer was located in a kitchen area, according to the deputy director-general of the National Parks department Adisorn Nuchdamrong.
He said: “They must be of some value for the temple to keep them. But for what is beyond me.”
Officials wore protective masks as they displayed the bodies of the cubs to media at the temple.
The images show dozens of tiger cub bodies laid out, with limp wet fur and blood stains.
Among the cub bodies was the carcass of a Binturong, a protected species commonly known as a bearcat, which was also found in the freezer.
The monks at the temple have not commented.
Officials say they have moved 52 live tigers from the temple since Monday, while 85 still remain.
The tourist destination lies west of Bangkok, but a long-running battle to take it under state control has rumbled on since 2001.
The organisation People for the Ethical Treatment of Animals (PETA) has described the temple as a “hell for animals” and urged tourists to stop visiting animal attractions at home and abroad.
Thailand is well known as a hub of illicit wildlife trafficking, and protected animals can sometimes be found for sale in markets.
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