Thai army chief Gen Prayuth Chan-ocha said he contacted the US military attache at the US embassy in Bangkok who apologised for the "misunderstanding" caused by the list, the Bangkok Post reported.
Department of Special Investigation (DSI) chief Tarit Pengdith disclosed the FBI's list yesterday.
The FBI had warned Thailand that it ranked at the top of the region as a possible terrorist target, Tarit said.
In researches conducted in the US and Britain, Thailand ranked fifth in the world as a possible target for terror attacks, Tarit said.
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"The information must be corrected straight away. The research is based largely on the number of violent incidents and casualties in the three southern Muslim majority border provinces," he was quoted by the Bangkok Post as saying.
He said the FBI had also asked Thai authorities to help arrest Jason Derek Brown, an American fugitive wanted by the FBI for allegedly murdering a security guard in an armed robbery of a cash-transport vehicle in Arizona in 2004.