Wildlife officials are continuing with their raid on the temple as they remove tigers from the facility in a move to bring the animals under state control.
On Thursday police caught a monk trying to flee the temple in a truck carrying animal skins and teeth.
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Hundreds of amulets containing tiger body parts, including a range of skins and fangs, were found in the vehicle.
A post on Tiger Temple's Facebook page reads: "The recent discovery of the tiger skins and necklaces comes as a shock to us as well as the rest of the world. We are disgusted at this discovery and we don't condone this.
"We are looking forward to the authorities bringing the culprits to justice."
Charity Wildlife Friends Foundation Thailand (WFFT) says that there are concerns as to the whereabouts of 20 live tiger cubs who are missing from the Tiger Temple.
The temple denies allegations that they have sold the cubs.
Tiger Temple promotes itself as a wildlife sanctuary, but in recent years it has been investigated for suspected links to wildlife trafficking and animal abuse.
Wildlife charities and animal welfare groups have been condemning the facility for years, as the temple grew in popularity with tourists wanting to have their photos taken with tigers.
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A raid that began on Monday is the latest move in a tug-of-war since 2001 to bring the tigers under state control.
Officials were not sure why the temple kept the cubs in the freezer.
“They must be of some value for the temple to keep them,” said Adisorn Nuchdamrong, deputy director-general of the Department of National Parks.
“But for what is beyond me."
More than 130 tigers were kept at the temple.
Thailand has long been a hub for the illicit trafficking of wildlife and forest products, including ivory.
And exotic birds, mammals and reptiles, some of them endangered species, can often be found on sale in markets.
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WFFT, a charity that has been working with Thai authorities and other NGOs to remove the tigers, said in a Facebook post on Thursday that staff at Tiger Temple have been dismissed, raising concerns about who will look after the animals.
The post read: "The abbot of the temple has fired all his staff, meaning there is now no longer Tiger Temple staff on site to take care of all the other animals, including domestic cattle, buffalo, deer and wild pigs.
"The WFFT along with Thai Animal Guardians Association are in talks with the authorities on how we can handle this situation and ensure that all the animals are cared for properly. What will the coming days bring."
On Tuesday, the People for the Ethical Treatment of Animals group said the temple was “hell for animals” and called on tourists to stop visiting animal attractions at home and abroad.
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The raids follow the controversial shooting of a gorilla at a Cincinnati Zoo on Saturday. The critically-endangered animal was killed after a child fell into its enclosure.
World Animal Protection said: “The cruelty towards tigers at the temple, and the latest scenes of dead cubs, is extremely disturbing.
“It’s clear that the welfare of the tigers is not a priority and their lives are full of abuse and commercial exploitation for the entertainment of tourists.”
The animal protection group commended authorities for taking action against the temple, but further urged the government to investigate how the cubs died, and to find an “appropriate safe environment” for the tigers it had already recused to spend the remainder of their lives.
Dario Pignatelli via Getty Images
A tiger looks one as a Thai DNP veterinarian officer assist it at the Wat Pha Luang Ta Bua Tiger Temple on June 1, 2016 in Thailand. Wildlife authorities raided a Buddhist temple in Kanchanaburi province where 137 tigers were kept, following accusations the monks were illegally breeding and trafficking endangered animals. Forty of the 137 tigers were rescued by Tuesday from the country's infamous 'Tiger Temple' despite opposition from the temple authorities
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Thai DNP officers carry a sedated tiger outside its cage at the Tiger Temple
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Thai DNP officers stand by caged tigers loaded onto a truck at the Tiger Temple
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Thai wildlife officials use a tunnel of cages to capture a tiger and remove it from an enclosure at the Tiger Temple
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Thai wildlife officials take a tiger away in a covered cage on a truck after they removed it from an enclosure at the Tiger Temple
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A Thai wildlife official speaks with a monk before officials removed tigers from enclosures
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Thai DNP veterinarian officers tend to a sedated tiger at the Tiger Temple
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A Thai DNP veterinarian officer assists a sedated tiger at the Tiger Temple
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Thai DNP veterinarian officers tend to a sedated tiger
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Thai DNP officers carry a sedated tiger outside its cage at the Tiger Temple
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Thai DNP veterinarian officers tend to a sedated tiger
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Thai DNP officers carry a sedated tiger at the Tiger Temple
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Thai DNP officers load a sedated tiger onto a truck
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Thai DNP officers carry a sedated tiger outside its cage at the Tiger Temple
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Thai DNP veterinarian officers tend to a sedated tiger at the Tiger Temple
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A tiger looks one as a Thai DNP veterinarian officer assist it at the Tiger Temple
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Thai DNP officers load a sedated tiger onto a truck
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Thai DNP officers load a sedated tiger onto a truck
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Thai DNP officers observe the carcasses of 40 tiger cubs and a bear found undeclared at the Tiger Temple
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Thai DNP veterinarian officers tend to a sedated tiger
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Thai DNP officers observe the carcasses of 40 tiger cubs and a bear found undeclared at the Tiger Temple
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Thai DNP veterinarian officers tend to a sedated tiger at the Tiger Temple
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A sedated tiger is ready to be carried away
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Thai DNP officers load a sedated tiger onto a truck at the Tiger Temple
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Thai DNP officers observe the carcasses of 40 tiger cubs and a bear
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Deputy DNP director-general Adisorn Nuchdamrong stands by the discovered carcasses
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A tiger peers through the bars of its cage at the Tiger Temple
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Thai DNP officers observe the carcasses of the discovered cubs
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A Thai DNP veterinarian officer holds the head of a sedated tiger
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The carcasses of 40 tiger cubs found undeclared at the Tiger Temple
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Thai DNP officers collect samples for DNA testing from the carcasses
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Thai DNP officers collect samples for DNA testing from the carcasses of 40 tiger cubs
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Thai DNP officers collect samples for DNA testing from the carcasses