Demosisto, which was set up by Mr Wong and fellow student activists earlier this year and now has a representative in parliament, said it "strongly condemns the Thai government for unreasonably limiting Wong's freedom and right to entry".
Chinese Foreign Ministry representatives have either said they had no specific knowledge of the repatriations or said they were handled in accordance with the law.
Thai immigration officials said they were reviewing the incident but denied detaining Wong.
Recounting his detention in a 50 sq ft cell at a police station in the airport, Mr Wong said: "I was anxious if I would become the next Gui Minhai or face a similar fate as the Causeway Bay booksellers". "China respects Thailand's [right to] exercise immigration control according to the law", an official at the embassy told The Nation.
Phnom Penh has received billions in civil and military aid from Beijing, seemingly in exchange for its efforts to tone down the Association of South-east Asian Nations' criticism of China's territorial ambitions in the disputed South China Sea. Last year Malaysia turned him away, reportedly over concerns his presence would damage ties with China.
The statement went on to say the Thai Ministry of Foreign Affairs was reviewing the facts of the case with the Immigration Bureau, and suggested Mr Wong would be deported back to Hong Kong and not to mainland China as some of his supporters had feared.
Wong said authorities took his passport and "illegally detained" him in a windowless holding cell at the Bangkok airport.
A 19-year-old political activist who achieved global prominence when he helped spearhead massive pro-democracy protests in Hong Kong against China's plan to restrict elections there in 2014 was barred from entering Thailand on Wednesday.
He then inquired at the Emirates counter and was told that Wong had been detained. He added that he would be demanding an explanation from the Thai government and that he would ask the Hong Kong government if it knew of the existence of any blacklist. "You have been blacklisted".
In January, Li Xin, a Chinese journalist, disappeared from Thailand.
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"So it's really out of my expectations to have this kind of suppression from the Thailand Government.""For me, I think this is illegal detention". In August, he escaped a jail sentence over the 2014 protests, after a Hong Kong court ordered him to perform community service instead. "We did not violate his rights but (we) facilitated him going back", he said.
"It's China's [internal] business".
Jason, who wrote a book on Hong Kong's umbrella movement protests, said, "He was most concerned about his personal safety, being abducted or attacked".
He said he was "totally disappointed" with the experience.
He was invited by Thai student activist Netiwit Chotipatpaisal to address students at Chulalongkorn University at Bangkok to mark the 40th anniversary of a students massacre in 1976.
CU student activist Netiwit Chotiphatphaisal, who was Wong's Thai host, said yesterday that Wong might still deliver his scheduled talk in Bangkok via Skype. He also said that the event was held only for academic purposes and did not have a political agenda.
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Thai Prime Minister Prayuth Chan-ocha said Wong's expulsion was a matter for China, not Thailand. "It is very unsafe here", one Chinese exile living in Bangkok said at the time.
"We do not agree with this action by the Thai government who are infringing on basic rights and stopping its citizens from acquiring knowledge about democracy".