Thani Thongpajkdi, the Thai foreign ministry's deputy spokesman, says the Thai authorities did escort the migrants back to sea.
"We are asking the agencies concerned what happened that led to the report, the allegations that came out," he told Al Jazeera.
"The government does not have a policy of treating these people inhumanely, or mistreating them. What we do is, when they arrive in the country, we get them provisions - we get them food, water, medicine, and then we escort them out.
"The [Thai] government does not have a policy of treating these people inhumanely, or mistreating them"
Thani Thonpakdi, Thai foreign ministry deputy spokesman
"Of course we're concerned for them but in escorting them out, we ensure that their vessel is seaworthy, we ensure that they have been given enough food, water, etcetera."
Abhisit Vejjajiva, the Thai prime minister, who has repeatedly stated a commitment to human rights and the rule of law, said on Thursday there were "quite a large number" of Rohingya in Thailand but that they were illegal immigrants and had to be "sent back".
Thousands of Bangladeshis and Rohingyas - members of a stateless, Muslim ethnic group that fled to Bangladesh to escape persecution in Myanmar - leave Bangladesh aboard rickety boats each year in hope of finding work in neighbouring countries.
UNHCR, the UN refugee agency, says as many as 230,000 Rohingya Muslims are now living a perilous, stateless existence just over the border in Bangladesh.
In the last three years, one of the most popular migration routes has been by boat to Thailand and then overland to Malaysia.
Reports from survivors who washed up on India's Andaman islands and northwest Indonesia suggest as many as 550 of the 992 towed out to sea by Thai soldiers are dead.
The men were headed from Bangladesh to Thailand when their boats were intercepted around December 27 by Thai naval ships.
In a detailed account of their experience, two survivors rescued by the Indian coastguard have told Arakan Project, a refugees' advocacy group, that they were detained and beaten by Thai authorities on Koh Sai Daen, a remote island in the Andaman Sea.
They were then abandoned in the Indian Ocean in boats with no engines and only a few bags of rice.
Arakan Project provided transcripts of their accounts on Friday to the Associated Press news agency.
'Handfuls of rice'
The migrants told Arakan that they survived on banana leaves and handfuls of rice while they on the remote island and that they were abused by armed guards they thought were from the Thai security forces.
"I was beaten with a stick while collecting banana plants for no reason," said a 20-year-old Bangladeshi, whose identity was concealed by the rights group.
"Other detainees arrested before us also complained they had been beaten without any reason."
The two survivors said they were then rounded up at night along with about 500 others and forced into four rickety boats with no motors.
The boats - each holding 150 people and provided with only a 25kg bag of rice and a few containers of drinking water - were tied to a navy ship and dragged for a day out into the high seas.
"When the sun disappeared in the horizon, they suddenly started cutting the rope that tied each boat to their ship," the Bangladeshi survivor said.
"Then, the navy boat made a U-turn and vanished in the dark of the night. We started drifting in the sea."
The two survivors said their food and water ran out after the first day and that the boat drifted in the open ocean for eight days. It was unclear if any of the 150 migrants on their boat died on the journey.
"We drifted for eight days and then we suddenly saw a hill. None of us was able to move because of severe dehydration and food deficiency," a 23-year-old Rohingya survivor said.
He said they survived for three days on coconuts before the Indian coast guard rescued them and took them to the Andaman islands.
Fears are also growing over the fate of 126 Rohingya boat people thought to remain in Thai military custody.
|The Thai navy has claimed it gave the Rohingya migrants food and water [AFP]
But the government says it no longer has any Rohingya migrants within its borders, 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," a Thai foreign ministry spokesman said.
He refused to answer repeated questions about the current whereabouts of the 126 and he did not say where, when and how they left the country.
The Isoc colonel at the heart of the abuse allegations has denied any wrongdoing.
The UNHCR asked Thailand on Tuesday to see the 126, most of whom it said were in army custody on an Andaman Sea island.
The office in Bangkok said on Friday it was still waiting for a formal response to its request, which was made on Tuesday.