The Department of National Parks, Wildlife and Plant Conservation will return 14 confiscated orangutans to Indonesia on Thursday, bringing the total number of apes sent back to the country since 2006 to 66.
Adisorn Noochdumrong, the department's deputy chief, said the move reflected the serious intentions of the two countries in dealing with wildlife crime.
They are following the code of practice under regulations by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (Cites), he added.
According to Cites, any confiscated wildlife must be sent back to the country of origin, while the country taking care of the smuggled animals is entitled to compensation from the home country.
However, Mr Adisorn said his department had agreed to waive the compensation of 3 million baht from Indonesia to strengthen their mutual cooperation.
But the Indonesian government will be responsible for the costs of transporting the primates home.
Thirteen of the orangutans were smuggled into Thailand five years ago by a wildlife trafficking ring.
Police believe they were destined for a private zoo; however, the traffickers panicked and left them on the side of a road in Phuket.
The department filed a police complaint and took the animals to the Khao Prathab Chang Wildlife Feeding Centre in Ratchaburi province. One baby orangutan has since been born.
DNA tests confirmed their origin as Kalimantan, and the Jakarta government was contacted to arrange their return.
Mr Adisorn said the department had completed quarantine and health checks required under international practices.
The return of the orangutans to Indonesia will be the third since 2006, he said.
An official source said the primates will be quarantined for four weeks at Taman Safari Park and rehabilitated at the Orangutan Rehabilitation Centre in Kalimantan, before being returned to the wild.