Rights groups have criticised the deportation of Muslim Uighurs saying they face persecution in China.
China denies repressing Uighurs and called the deportees illegal migrants.
There have been days of unrest in Turkey over reports of Uighurs in western China being restricted by the Chinese government from observing the holy month of Ramadan.
Uighurs have close cultural and religious ties with Turkish Muslims.
Protests outside the Chinese embassy have seen Chinese flags burnt and on Thursday police fired pepper spray at demonstrators.
There have been reports of Chinese citizens being harassed and attacked and China issued a travel warning to its citizens travelling to Turkey.
Thailand`s decision to deport about 100 Uighurs has raised tensions further.
Windows at the Thai consulate were smashed, furnishings damaged and the sign outside pulled down.
Thai spokesman Werachon Sukhondhapatipak told reporters the government had ordered the embassy and consulate to close temporarily on Friday.
He added: "We will assess the situation on a daily basis."
About 400 Uighurs detained for illegally entering Thailand in March last year have been the focus of a diplomatic dispute between Turkey and China over where they should be moved to.
Thailand said about 100 people were removed on Wednesday, while an earlier group of 172 women and children were sent to Turkey in late June.
China`s foreign ministry spokeswoman Hua Chunying confirmed at a news conference the return of minority ethnic citizens in recent days.
She said it had been determined after a joint investigation with Thailand that the deportees were "illegal migrants".
She said some foreign countries were ignoring such "facts" and calling them refugees which "breaks international conventions and laws".
She also denounced attacks on Chinese citizens in Turkey.
Chinese state media has reported that the group may have been on its way to join Islamist militants in Syria and Iraq which BBC Shanghai correspondent John Sudworth said would probably heighten fears about what China will do with them.
The United States and the United Nations refugee agency have condemned the deportation.
"They could face harsh treatment and a lack of due process," the US State Department said.
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