Thailand has yet to approach Indonesia about joining the southern peace process officially, but cooperation is ongoing at the operational level, National Security Council (NSC) chief Paradorn Pattanatabut says.
The Indonesian embassy in Bangkok on Friday denied that Jakarta was involved in the NSC-led peace process.
"As far as the Indonesian embassy is concerned, the government of Indonesia is not yet aware about the request from the NSC," the embassy's First Secretary Ghofar Ismail said.
Lt Gen Paradorn, however, said there has already been cooperation, albeit in an informal manner.
In early April, his deputy Adisak Tanyakul and secretary-general of the Southern Border Provinces Administration Centre (SBPAC) Thawee Sodsong travelled to Indonesia to meet members of its national security team, Lt Gen Paradorn said.
Mr Adisak and Pol Col Thawee brought religious leaders from Yala, Pattani and Narathiwat to meet with moderate Islamic leaders in Indonesia, he said.
The Indonesian embassy also denied the NSC's claim that many young militants in Thailand's deep South have received training in Indonesia. It said the assertion is "inaccurate and unacceptable".
"This accusation definitely will not contribute anything to the settlement of the already complex issue in the southern provinces," the embassy said.
The embassy added that it has asked Thailand to present information about the alleged insurgency training in Indonesia but it had not received any confirmation it was taking place.
Lt Gen Paradorn admitted that he has not informed the Indonesian government of the insurgents' movement there as he does not have solid evidence.
He insisted, however, that Thai intelligence reports indicate connections with Indonesia.