Rohingya arriving in Thailand risk falling into the hands of people smugglers who demand large sums of money to transport them to Malaysia, while those unable to pay are believed to be forced into labour to pay the fees.
"There were army officials involved -- some local unit heads," a senior Thai intelligence official who did not want to be named told AFP.
Normally Rohingya come ashore on Thailand's southwestern Andaman coast but recently they have been found in the province of Songkhla bordering Malaysia on the other side of the peninsula, he said.
"They could not be there if there were no government officials involved. The trafficking will involve brokers. They could have paid 40,000-60,000 baht ($1,350-2,000) to travel to Malaysia overland," the official added.
National Security Council secretary general Paradorn Pattanathabutr said the army was investigating the claims, which first appeared in local media, but up to now had found no evidence of wrongdoing.
"If we found somebody guilty, they will be punished," he added.
Described by the UN as among the most persecuted minority groups in the world, Rohingya have for years trickled abroad to neighbouring Bangladesh and, increasingly, to Muslim-majority Malaysia.
Myanmar views its population of roughly 800,000 Rohingya as illegal Bangladeshi immigrants and denies them citizenship.
A explosion of tensions between Buddhist and Muslim communities in Myanmar's western state of Rakhine since June 2012 has triggered a huge exodus of Rohingya, mostly heading for Malaysia.
The UN estimates that about 13,000 boat people fled Myanmar and Bangladesh in 2012 with some dying during the perilous sea voyage. Hundreds have been detained inThailand in recent weeks.
Buddhist-Muslim clashes have left at least 180 people dead in Rakhine since June. More than 110,000 people, mostly Rohingya, have been displaced.
A spokesman for Thailand's Internal Security Operation Command, whose officers have been accused by local media of involvement in the people smuggling, said he was aware of the allegations but could not confirm or deny them.
"We have to investigate but up to now we don't have any information," he said.