The government knew two Chinese men it detained were refugees awaiting resettlement in Canada, but still deported them to China, according to a United Nations letter seen by Reuters.
The letter, sent by the UN High Commissioner for Refugees (UNHCR) to the Ministry of Foreign Affairs, contradicts Thai Prime Minister Prayut Chan-o-cha's statement last week that Thailand "did not know" that the men were under UNHCR protection.
Thailand has been criticised for deporting the two dissidents, Jiang Yefei and Dong Guangping, at Beijing's request in mid-November, despite both being recognised as refugees.
Gen Prayuth last week said China had arrest warrants out for the men. Reuters could not confirm this.
Rights groups have denounced Communist Party rulers in China for their secretive system of detention of dissidents and lack of an independent judiciary to ensure fair trials. China says it follows the rule of law.
Thailand drew international criticism in July when it deported more than 100 Uighur Muslims to China. The Uighurs are a Turkic-speaking minority from China's troubled western Xinjiang region and rights groups said the deportees could face ill-treatment at home.
Mr Jiang and Mr Dong, who were arrested by Thai authorities on Oct 28, were awaiting resettlement in Canada. They were deported back to China on Nov 14 or 15, and their current whereabouts were unknown.
A Chinese state newspaper reported they were being detained.
In the letter, dated Nov 16, the UNHCR raised its objections to the deportations and reminded the foreign ministry that it had informed the government in writing on Nov. 10 that the men were refugees and had been accepted for rapid resettlement by Canada.
The letter said it had written to the Justice Ministry, immigration bureau, Foreign Ministry and National Security Council.
The UNHCR had previously asked Thai authorities to suspend the deportation of the men, and had kept the government fully informed of their legal status, the letter said.
Vivian Tan, a spokeswoman for the UNHCR in Bangkok, told Reuters the agency was unable to comment on individual cases or its engagement with the government.
"What I can confirm is that we were not informed of the deportation beforehand," she said in an email.
Gen Prayut said last Tuesday that Mr Dong and Mr Jiang were arrested for violating Thai immigration law, and were found to have outstanding Chinese arrest warrants.
"The foreign ministry was not aware about the third country settlement," Sek Wannamethee, a ministry spokesman, told Reuters on Monday.
"Thailand will continue to work closely with our international partners including the UNHCR toward a more systematic screening mechanism to help make these decisions more efficient with a clear guideline for relevant agencies," he said.
A Bangkok-based diplomat, who declined to be named because of the sensitivity of the matter, told Reuters the Foreign Ministry had been told "several times" that the men were refugees before they were deported.
Thailand has drifted closer to China since the military seized power in Bangkok in May last year in a coup that was criticized by Thailand's traditional partner, the United States. The Thai and Chinese air forces conducted their first joint exercises last week, billed by Beijing as promoting "mutual trust and friendship".
The decision to deport the men appeared to have been made at high levels of Thailand's military government, the diplomat said, cutting out the foreign ministry which appeared to have only been aware of the deportations after the two men had left the country.
"We are concerned that this goes against Thailand's international obligations with respect to non-refoulement," he said, referring to the principle of not returning someone to a country where they are liable to be subjected to abuse.