The bodies of the cats were discovered in a freezer at the Wat Pha Luang Ta Bua Tiger Temple which has been accused of wildlife trafficking and animal abuse.
An operation began on Monday to remove all tigers from the popular tourist site, which had allowed visitors to feed the animals and take photos for a fee, in spite of the fact that the temple supposedly being banned from charging admission fees or money.
It has been closed to visitors since the raid.
According to the BBC, body parts of other creatures were also revealed during the search of the property including animal intestines and a dead boar.
Speaking about the discovery of the dead cubs, deputy director-general of the Department of National Parks, Adisorn Nuchdamrong told Reuters: "They must be of some value for the temple to keep them, but for what is beyond me."
Tom Taylor, from the Wildlife Friends Foundation, who was at the temple in the Kanchanaburi district of the country, told the BBC that 40 living tigers had so far been rescued out of the 137 kept at the temple.
Authorities have been in a dispute with the monks at the site over confiscating the animals since 2001, after allegations of trafficking and mistreatment surfaced.
The monks have denied any wrongdoing.
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