Pictures posted on social media showed the 40 dead cubs lined up on the floor. The site has been closed for public since the raid.
Monks at the temple have previously denied trafficking allegations.
But police and wildlife officials started an operation on Monday to relocating its 137 tigers, mostly Bengal tigers.
In the first batch, more than 100 tigers will be taken away from Wat Pa Luangta Bua Yannasampanno, popularly known as the Tiger Temple, said the Department of National Parks, Wildlife and Plant Conservation.
The temple authorities have been accused of being involved in illegal wildlife trade and animal mistreatment for almost a decade by government officials and animal rights activists.
Suphitphong Phakcharung, vice-president of the Wat Pa Luang Ta Bua Foundation, said the group opposed to the action because the temple had raised the tigers for more than 10 years without a problem.
"We are trying to solve problems step by step," he said.
The department hopes to relocate all 137 tigers in seven days. Most of the tigers will be sent to the Khaoson and Khao Prathap Chang breeding centers in Ratchaburi province.
However, due to the temple's attitude, Adisorn admitted that the operation may take longer than seven days.
Tensions were running high at the temple on Monday as officials and temple representatives met.
Kasetsart University Faculty of Forestry lecturer Anak Pattanavibool said the authorities were right to relocate the tigers because the state was the animals' rightful owner.
"We cannot give them to a zoo or other countries because they are the government's property, so the government has to keep them until they naturally die," he said.
