Local authorities confirmed that 54 would-be refugees were in the vessel that was intercepted near Ra island, close to the fishing port of Kuraburi, north of Phuket.
A group of 92 boatpeople, apprehended nearby on November 24, was trucked north to the Thai-Burma border in police vehicles to be handed over at some point in unconventional circumstances to the Thai Army.
Today, the Thai Army picked up the 54 would-be refugees in an Army vehicle before carrying them off to an unknown destination.
Local authorities said that the Army's Internal Security Operations Command was involved in today's operation. An Isoc officer had given orders not to talk to the media or send on photographs, one official said by telephone.
As with the 92 men and boys apprehended on November 24, the likely destination and fate of the 54 boatpeople captured today is not known and unlikely to be revealed by Isoc.
Thailand's policy towards the Rohingya boatpeople has again become covert and increasingly of concern to United Nations organisations and international aid groups.
Four days after the first 92 boatpeople vanished, Human Rights Watch called on the Government of Thailand to disclose their whereabouts and explain the Army's role in the unconventional apprehension and detention of the group.
After January 2009, when the South China Morning Post newspaper in Hong Kong and Phuketwan revealed that large numbers of boatpeople were being towed out to international waters and cut adrift by the military and paramilitary, the detention of unwanted arrivals by sea on Thailand's coast reverted to Immigration officials.
More boatloads of Rohingya are reported to have sailed from northern Burma or Bangladesh in recent days, disenchanted at the lack of change in the ''new'' Burma, where they remain deprived of citizenship and controlled by repressive measures.
The US was previously one of the Rohingya's strongest public and private advocates.
However, official calls for a change in attitude towards the Rohingya in Burma and Thailand have not been made for some time.
US Secretary of State Hillary Clinton met with government leaders and opposition democracy icon Aung San Suu Kyi in Burma this week.
Human Rights Watch deputy Asia director Phil Robertson said today that Thailand's ''apparently discriminatory'' policy in dealing with the Rohingya gave comfort to the Burmese Government.