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.
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.
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."
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 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.