The men were identified as Sulaiman Madadam, 58, and Yagop Heemhame, 46. Police are looking for the men, who are natives of Songkhla.
Police have charged the former with providing shelter to the migrants and the latter with bringing them to Thailand, Pol Maj Gen Thatchai Pitaneelabutr, Songkhla Immigration Office chief, said on Wednesday.
Pol Maj Gen Thatchai did not explain how the suspects brought the suspected Muslim Uighurs into Thailand.
But he said police are collecting evidence to substantiate charges dealing with human trafficking against their boss whose first name begins with the Thai letter ''Wor Wan'' before issuing another arrest warrant.
In addition, further investigations are underway to link the smuggling of these suspected Muslim Uighurs with an international human trafficking gang, he said.
Pol Maj Gen Thatchai said Thai, Chinese and Turkish authorities are working together to identify the migrants' origins and nationalities. However, they still claimed they were travelling to Turkey via Thailand.
He said the Turkish embassy in Thailand sent staff to verify the nationalities of the migrants, who are now sheltered at two different locations in Songkhla. Chinese authorities also urged Thai authorities to verify their origins.
The 218 suspected Muslim Uighurs were divided into three groups. Sixty-nine Uighur men have been detained at Padang Besar Immigration Office and 54 Uighur women and 95 Uighur children were at a temporary shelter of the Social Development and Human Security Ministry, he said.
"No matter where they are from, we will try to deport them back to their country,'' he said.
However, police suspect they are ethnic Uighurs from China's northwestern Xinjiang region.
Pol Maj Gen Thatchai said his investigators had talked to them through an Arabic interpreter, saying they did not want to stay in China, but wanted to go to Turkey.
If it is proven the migrants are Muslim Uighurs from China and they do not want to return to China, they can ask the United Nations High Commissioner for Refugees to help send them to Turkey. But if it is found they hold dual nationalities, they can travel to Turkey and live there, he said.
"While waiting for the nationality verification, we will treat them equally under human rights principles,'' he said.
Pol Maj Gen Thatchai said investigators found the migrants had no terrorist links and simply entered Thailand illegally. Their arrests cost this human trafficking gang about 50 million baht, he said.
Chinese embassy spokesman and counsellor Yin Haihong said China was concerned over the arrest of those suspected of being Muslim Uighurs. But China has yet to verify their nationality.
Chinese ambassador to Thailand Ning Fu Kui on Tuesday met national police chief Pol Gen Adul Saengsingkaew to discuss the investigation's progress.
A source said the migrants are wealthy. They sold all of their assets in China to move to Turkey.
The source said each migrant paid around 100,000 baht to a human trafficking broker who brought them into Thailand. Parents paid 50,000 baht per child. Each had to pay an extra 60,000 baht if they needed fake Turkish passports.