'Abused and exploited'
Reports from survivors who washed up on India's Andaman islands and northwest Indonesia suggested as many as 550 of the 992 towed out to sea by Thai soldiers later died.
Myanmar refuses to recognise the Muslim Rohingya minority in western North Rakhine state as a distinct ethnic group.
Human rights activists say they have been abused and exploited, forcing many to flee abroad, mainly across the border to Bangladesh.
Thousands of Rohingya and Bangladeshis leave the country aboard rickety boats each year in hopes of finding work, with many travelling to Thailand by sea and then overland to Malaysia.
Villagers in Kura Buri on Thailand's southern coast told Al Jazeera on Saturday that they were also asked to remove the engine of a boat with Rohingyas on board before it was towed back out to sea.
| The Thai government has denied holding 126 Rohingya on Andaman sea island [AFP]
It is unclear what happened to the people on the vessel in December.
On Thailand's Andaman coast, Al Jazeera's Selina Downes also found decaying boats that had been dumped by Thai authorities.
Local villagers said that one boat had recently been discovered carrying about 46 Rohingya who had spent almost two weeks travelling from Bangladesh.
The fate of 126 Rohingya refugees is still unknown, but according to the UNHCR, they are thought to be in Thai military custody.
The UN refugee agency asked Bangkok on Tuesday to be allowed to visit the 126 refugees, most of whom it said were detained on an Andaman Sea island.
The foreign ministry said that was no longer the case, citing the army's Internal Security Operations Command (ISOC), which admits to overseeing the arrest and detention of the group of Rohingya.
"The latest information that we have from ISOC is that there are no longer any Rohingya left in Thailand," said Thani Thongpajkdi, the deputy ministry spokesman.
He also refused to answer repeated questions about the current whereabouts of the 126, or say where, when and how they left the country.