Thai wildlife officials have discovered dozens of dead cubs at a controversial "tiger temple" that has been locked in a long-running dispute with authorities and animal rights groups, police said Wednesday.

Wildlife officials found the tiger cubs during a continuing operation to remove dozens of adult cats from the Wat Pha Luang Ta Bua temple in the western province of Kanchanaburi.

"We found 40 tiger cubs today, they were aged about one or two days when they died but we don't quite know yet how long they have been dead," police colonel Bandith Meungsukhum, a local officer, told AFP. 

He added that wildlife officials would file a new criminal complaint following the discovery.

The temple has long proved a hit among mainly foreign visitors who flock there to be photographed -- for a fee -- next to the scores of exotic feline pets.

Wildlife officials say the whole complex is illegal and have battled the monks for years to try and close it down. The dispute has been complicated by the fact that secular Thai authorities are often reluctant to intervene in the affairs of the clergy.

This week officials were granted a court order to seize the cats and have so far removed more than 30 adults.

Animals rights groups have accused the temple of complicity in the hugely lucrative black-market wildlife trade, making tens of thousands of dollars by selling off older cats and animal parts for use in Chinese medicine.

Last year one of the temple vets turned whistleblower, handing authorities three microchips he said were inside a trio of tigers who had disappeared. It has never been fully established what happened to those tigers.

In February 2015 wildlife officials also conducted a raid and discovered dozens of hornbills, jackals and Asian bears that were being kept at the sanctuary without permits.

The temple has always denied trafficking allegations. 

In a statement posted on its Facebook page, the temple said it was common for cubs to be stillborn or die shortly after birth.

The temple said it used to cremate dead cubs but the policy was changed in 2010. 

"Instead of cremation, the deceased cubs were preserved in jars or kept frozen," the statement added, without elaborating on why the policy was changed.

The temple also denied selling cubs, saying such rumours were from people who have "jumped to conclusions".

Moves to confront the monks and confiscate the tigers have been staggered over recent months. There are now believed to be around 100 tigers remaining at the temple.

For years the government has been seemingly powerless to resolve the issue, partly for fear of being seen to confront the clergy and also because officials readily admit they have nowhere else to put such a large number of tigers.