Dozens of police and park officials have been stationed at the Wat Pha Luang Ta Bua temple in western Kanchanaburi province since Monday after receiving a court order to remove over 100 adult cats from the complex.
For decades the infamous temple has been a popular stop for tourists who pay a steep fee to pet and be photographed with the predators - which animal rights groups say are heavily sedated.
In addition to more skins that were later found in monks' quarters, officials discovered a live lion, hornbill, sun bear and banteng (an endangered species of wild cattle) inside the temple compound.
They also uncovered around 20 jars of preserved tiger parts containing "both whole bodies and organs to be use for medicines," Adisorn said.
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The discovery comes after authorities found dozens of dead tiger cubs inside a freezer at the temple yesterday.
Repeated efforts to shut down the temple over the years have been delayed and complicated by the fact that secular Thai authorities are often reluctant to intervene in the affairs of the clergy.
The temple has always denied trafficking allegations.
Officials said they have removed 84 tigers so far this week and are transferring the animals to nearby breeding centres.
No criminal charges have been filed against the temple yet, according to police.