The UN refugee agency estimates that about 1,000 Burmese political refugees have missed Thursday's deadline to register with the Thai authorities.
These refugees could now be detained and deported back to Burma.
Those who did register are now being sent to special camps along the Thai-Burma border.
The UN has expressed its concern about the refugees, and the conditions in some of the camps. Rights groups say the relocation is a political move.
They say the Thai government, which has been forging closer links with Burma's military junta, wants to weaken the country's international pro-democracy movement.
No mobile phones or other electronic devices will be allowed into the camps, making it difficult for political activists to continue their work.
As he boarded a bus in Bangkok to take him to a camp, Khin Maung Win, a former political prisoner in Burma, told the Associated Press he felt as though he were being imprisoned again.
Another dissident, Kuang Zan, told the Bangkok Post he was not sure the camps would be safe.
"The [pro-Rangoon] Democratic Karen Buddhist Army has already broken into some refugee camps, and hurt some of the refugees there," he said.
Some 3,000 refugees were expected to eventually take part in the relocation programme, according to the UN.
On Thursday, the deadline for registration, about 250 people signed up at a detention centre near Bangkok while another 400 registered in the north-western border town of Mae Sot, according to the UN High Commission for Refugees
Douglas DiSalvo, a official for the UNHCR, which is overseeing the programme, said: "We had a steady flow of people throughout the day. People came in all different vehicles - people in trucks and taxis and private cars, with all their belongs and bags ready for transport to the camps."
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