Prime Minister Prayuth Chan-ocha also raised the possibility of shutting the Thai Embassy in Turkey after protesters attacked the honorary consulate in Istanbul, smashing windows and ransacking parts of the building, over the expulsion of the Uighurs back to China.
China`s treatment of its Turkic language-speaking Uighur minority is a sensitive issue in Turkey and has strained bilateral ties ahead of a planned visit to Beijing this month by President Tayyip Erdogan.
Some Turks see themselves as sharing a common cultural and religious heritage with their Uighur "brothers" and Turkey is home to a large Uighur diaspora.
"I ask that we look after the safety of the embassy staff first," Prayuth told reporters. "But if the situation gets worse then we might temporarily have to close the embassy in Turkey."
Hundreds, possibly thousands, of Uighurs keen to escape unrest in China`s western Xinjiang region have travelled clandestinely via Southeast Asia to Turkey. China is home to about 20 million Muslims spread across its vast territory, only a portion of whom are Uighurs.
"Thailand sent around 100 Uighurs back to China yesterday. Thailand has worked with China and Turkey to solve the Uighur Muslim problem. We have sent them back to China after verifying their nationality," Colonel Weerachon Sukhondhapatipak, deputy government spokesman, told reporters on Thursday.
A group of more than 170 Uighurs were identified as Turkish citizens and sent to Turkey, he said. Fifty others still need to have their citizenship verified.
"If we send them back [to China] and there is a problem that is not our fault," said Prime Minister Prayuth, the general who led a coup against Thailand`s elected government in May 2014.
The United States condemned the deportations and asked Thailand to stop them, saying the Uighurs could face harsh treatment in China, State Department spokesman John Kirby said.
"We strongly urge the government of Thailand, and other governments in countries where Uighurs have taken refuge, not to carry out further forced deportations of ethnic Uighurs," Kirby said in a statement. He also urged China to ensure proper treatment of the Uighurs.
Hua Chunying, a spokeswoman for China`s foreign ministry, would not confirm whether the Uighurs had been deported to China but spoke in general terms about the issue at a daily news briefing in Beijing on Thursday, saying the Uighurs were "firstly Chinese".
Beijing denies restricting the Uighurs` religious freedoms and blames Islamist militants for a rise in violent attacks in Xinjiang in the past three years in which hundreds have died.
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