Bangkok (CNN) Authorities have discovered the remains of 40 newborn tiger cubs in freezers at the controversial "Tiger Temple," in Kanchanaburi Province, west of Bangkok.

An antler from a deer and the body of a binturong -- a Southeast Asian bearcat -- as well as a cow horn were also discovered.

The Wildlife Conservation Office (WCO) is investigating the motives behind the temple storing the bodies and is looking into the possibility that it is smuggling tiger parts, the organization's director, Teunjai Noochdumrong told CNN.

The discovery of the cubs' bodies is, she says, further evidence that the facility broke an agreement that they would inform the WCO if new cubs were born at the temple.

The organization believes the temple's license to keep tigers should be revoked.

"We are determining if we will file a legal suit against the temple," Noochdumrong said.

If they are found attempting to smuggle the tiger cub remains, temple officials could face up to four years in jail and or be fined up to $1,121 (THB40,000), she added.

The vice-president of the temple foundation, Suthipong Pakcharoong, did not immediately respond to phone calls from CNN.

Tiger-catching 'mayhem'

The operation to remove the tigers began on Monday. On Tuesday, authorities armed with tranquilizer guns were trying to capture dozens of tigers at the controversial Buddhist temple after staff allegedly set some free to delay the process.

As of Wednesday, the organization's staff had caught 52 tigers. The temple housed a total of 137 tigers.

Noochdumrong described it as "mayhem" Tuesday.

"When our vet team arrived, there were tigers roaming around everywhere," Noochdumrong said. "(It) looks like the temple intentionally let these tigers out, trying to obstruct our work."

The temple has long been popular with tourists , who could walk among the tigers and pose for photos. The WCO said the temple's tigers posed a danger to visitors and that they were being mistreated.

A tourist poses for a photo with a tiger at the Thai temple in 2012.

When staff from the WCO arrived Monday morning to remove the tigers, temple officials refused to let them in. After a half-day standoff, wildlife officers finally entered and were able to sedate eight tigers.

On Wednesday the WWF released a statement "applauding" the removal of the tigers, and encouraging the Thai government to permanently revoke their license to keep the animals.

"This week's actions to remove the tigers from the Tiger Temple are long overdue and we strongly encourage DNP (the Thai Department of National Parks, Wildlife and Plant Conservation) to make the removal of the tigers permanent," said Yowalak Thiarachow, Country Director, WWF-Thailand.

Other facilities with captive tigers should also be investigated, the statement adds, to ensure the animals are not victims of wildlife trafficking and abuse.

According to the DNP, the country has around 1200 - 1300 captive tigers in at least 33 facilities.

Capture in progress

The conservation office received a search warrant from a local court following failed negotiations with representatives from Wat Pha Luang Ta Bua Temple, as the Tiger Temple is officially known. The temple says it is a sanctuary for wild animals.

Over 2,000 personnel, including veterinarians, WCO civil servants, provisional police and local military are taking part in the mission to relocate the tigers to a compound in Ratchburi Province.

Suthipong Pakcharoong, the vice president of the Wat Pha Luang Ta Bua Temple Foundation, told CNN Tuesday that the temple would comply with the court order but the relocation of the tigers would have a negative impact on the local economy.

"There is nothing illegal and dangerous at all," said Pakcharoong. "If they do like this, it would affect the tourism industry."

Photos: Thai authorities remove tigers from temple National Parks and Wildlife officers examine a tiger skin at the "Tiger Temple," west of Bangkok, Thailand on Thursday, June 2. Thai police say they stopped a truck carrying two tiger skins and other animal parts as it was leaving the temple. Two staff members were arrested and charged with possession of illegal wildlife. Hide Caption 1 of 18 Photos: Thai authorities remove tigers from temple Bone products are laid out on a table by National Parks and Wildlife officers at the "Tiger Temple," west of Bangkok on June 2. Hide Caption 2 of 18 Photos: Thai authorities remove tigers from temple Thai wildlife and conservation officials display more animal parts found at the controversial Buddhist temple on June 2. Hide Caption 3 of 18 Photos: Thai authorities remove tigers from temple Hide Caption 4 of 18 Photos: Thai authorities remove tigers from temple Jars containing baby tiger parts found at Wat Pha Luang Ta Bua Temple on June 2. Hide Caption 5 of 18 Photos: Thai authorities remove tigers from temple National Parks and Wildlife officers display the skins from two tigers that were seized from a truck leaving the temple, June 2. Hide Caption 6 of 18 Photos: Thai authorities remove tigers from temple Thai wildlife officials collect samples for DNA testing from the carcasses of 40 tiger cubs and a binturong, or a Southeast Asian bearcat, found at the temple on June 1. The government's Wildlife Conservation Office is looking into the possibility that the temple is smuggling tiger parts, the organization's director told CNN. Hide Caption 7 of 18 Photos: Thai authorities remove tigers from temple Veterinarian officers with Thailand's Department of National Parks, Wildlife and Plant Conservation tend to a sedated tiger at the controversial "Tiger Temple" in Kanchanaburi province on Wednesday, June 1. Authorities raided the compound over concerns about the welfare of the animals and complaints from tourists. Hide Caption 8 of 18 Photos: Thai authorities remove tigers from temple Tigers are loaded onto a truck at the temple on June 1. Hide Caption 9 of 18 Photos: Thai authorities remove tigers from temple Thai officers load a sedated tiger onto a truck on June 1. Hide Caption 10 of 18 Photos: Thai authorities remove tigers from temple Veterinarian officers tend to a sedated tiger on June 1. Hide Caption 11 of 18 Photos: Thai authorities remove tigers from temple Thai officers carry a sedated tiger from its cage on June 1. Hide Caption 12 of 18 Photos: Thai authorities remove tigers from temple Thai wildlife officials use a tunnel of cages to capture a tiger and remove it from the temple on Monday, May 30. Hide Caption 13 of 18 Photos: Thai authorities remove tigers from temple A Thai wildlife official speaks with a monk at the temple. Hide Caption 14 of 18 Photos: Thai authorities remove tigers from temple The temple is home to 137 tigers. A wildlife official said when they finally entered the compound, monks had left the cages open and unchained the tigers to stall their removal. Hide Caption 15 of 18 Photos: Thai authorities remove tigers from temple Veterinarians prepare anesthetic syringes used to sedate the tigers. Hide Caption 16 of 18 Photos: Thai authorities remove tigers from temple Thai wildlife officials load a sedated tiger into a cage on a truck. Hide Caption 17 of 18 Photos: Thai authorities remove tigers from temple Thai wildlife officials carry a tiger on a stretcher from the temple. Hide Caption 18 of 18

Questionable conditions

Thai authorities have long been under pressure to stop the business.

"We have been receiving complaints from tourists they were attacked by tigers while walking (among) them at the temple," said Noochdumrong. "We had warned them to stop this act; they didn't listen."

As part of a 2001 agreement with the WCO, the temple was allowed to take care of the tigers as long as it didn't use them for profit or breed them.

However, the tigers were also allowed to breed freely, and many of them suffer from chronic illnesses and blindness, according to WCO.

The temple's tigers seen playing with a water bottle. The sanctuary had received criticism over the welfare of the animals.

The temple also charged tourists to enter the compound and walk with the big cats, however Pakcharoong said the money was used to pay for the tigers' care.

"We have to do that because that is how we earn the money and use that money to take care and raise our tigers," said Pakcharoong.