"The Thai government and the neighbouring administration have to find an appropriate way to ensure a safe return of the refugees," the English-language daily quoted Gen Prayuth as saying in his televised weekly address late on July 25.
"The significant matter is that is that human rights must not be violated," said Gen Prayuth, who has been appointed prime minister since the military seized power in a coup on May 22.
The Bangkok Post report also quoted Gen Prayuth as saying that the Thai authorities were yet to begin the repatriation of Myanmar refugees in Thai camps.
Without giving any indication when repatriations would begin, the Thai junta leader said they would not be conducted by members of the Thai armed forces.
Gen Prayuth's comments were an apparent attempt to assuage concerns raised by refugees and non-government organisations that residents of the nine official camps along the border with Myanmar would be forcibly repatriated.
Concerns have risen during the past month because the Thai authorities have been enforcing restrictions on movement outside the camps and have begun head-counts of their residents.
They rose further when Gen Prayuth said in the aftermath of a visit to Thailand by Myanmar Commander-in-Chief Senior General Min Aung Hlaing earlier this month that refugees from the nine camps would be repatriated.
The Bangkok Post said repatriation was expected to be on the agenda during a three-day Thai-Myanmar Regional Border Committee meeting due to begin at Myeik in Tanintharyi Region on August 1.
On another issue involving Myanmar living in Thailand, Gen Prayuth said the Thai authorities were working with the governments of neighbouring countries to arrange a smoother process for issuing passports to undocumented migrant workers.
There has criticism from migrant rights groups in Myanmar that the process for obtaining documents necessary to work in Thailand legally was too complicated.