The temporary closure of Thailand's embassy in Ankara and consulate in Istanbul comes after anti-Chinese demonstrators stormed the latter, damaging furnishings and pulling down the sign outside.
It was the latest protest in Turkey over the treatment of the Turkic-speaking, largely Muslim minority in China's northwestern Xinjiang region, where Uighurs say they face cultural and religious repression.
Read: Thailand deports scores of Uighur Muslims to China, sparks safety fears
Scores are believed to have fled the restive area in recent years, sometimes travelling through Southeast Asia in hope of resettling in Turkey.
In Thailand the fate of some 400 Uighurs had been shrouded in uncertainty since March 2014 when they were detained for illegal entry while authorities verified their nationalities amid a tussle between Turkey and China over where they should be moved.
The junta-ruled kingdom revealed Thursday that around 100 Uighurs were deported to China on Wednesday, while an earlier group of 172 women and children were sent to Turkey in late June.
Read: China says tourists attacked in Turkey during anti-China protests
News of the sudden China deportations sparked international condemnation including from the United States, rights groups and the UN as well as the Istanbul protest.
In Bangkok, Thai government spokesman Werachon Sukhondhapatipak told reporters on Friday that "the government has ordered the Thai embassy and consulate to close temporarily today".
"We will assess the situation on a daily basis," he said, adding all was currently under control with no Thai nationals affected, while citizens had been warned to remain on alert.
According to a Turkish news agency, an Asian tourist was attacked by pro-Uighur protesters in Ankara Thursday as they thought she was Chinese.
Responding to criticism over the China deportations, Werachon said that high-level Thai officials would travel to the country next week to follow-up on the returned group.
Uighurs in Xinjiang, who number around 10 million, have long said they face discrimination. More recently China has launched a wide-ranging crackdown in the region in response to rising violence which authorities blame on Islamist separatists.
Under pressure from Beijing, countries including Cambodia, Malaysia and Pakistan have all in recent years forcibly returned members of the ethnic minority to China.
On Thursday the United States expressed "grave disappointment" in Thailand.
"We condemn Thailand's forced deportation on July 9 of over 100 ethnic Uighurs to China, where they could face harsh treatment and a lack of due process," the State Department said in a statement.
The UN says the deportation was a violation of international law, referring to the principle of non-refoulement which prohibits the transfer of people to a place where they are at risk of rights abuses.
But Thai premier Prayut Chan-O-Cha on Friday defended the legal status of the repatriation because China had "guaranteed their safety".
"If found innocent they will be released," he told reporters.
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