No explanation was immediately given.
Sidney Jones, the project director for the International Crisis Group in Jakarta, said she was refused entry to the country on Thursday on return from a trip to Taiwan.
"I received no explanation and no warning that it was going to happen," she said on Friday from Singapore.
Jones' Brussels-based think-tank opened an office in Indonesia in 2000 and has released detailed and well-researched reports on the activities of the al-Qaida linked group Jemaah Islamiyah.
The regional extremist network has been blamed for at least four deadly bombings in Indonesia, including last month's triple suicide attacks on the resort island of Bali that killed 20 people.
Jones was also expelled from Indonesia in 2004 under the administration of president Megawati Sukarnoputri for allegedly publishing false reports damaging to the country's image.
President Susilo Bambang Yudhoyono's government allowed her to return in July.
Indonesian Foreign Ministry spokesman Yuri Thamrin said he was told by immigration officials that Jones had been barred from the country, but was given no reason.
Jones is known for her work on
Jemaah Islamiyah's leadership
Jones said when she arrived in Jakarta after attending a Time magazine awards ceremony honouring her think-tank, she was told that a 7 October letter banned her from entry.
"I don't understand," she said, adding that she has been in and out of the country several times in the last six weeks.
"If there was a problem, you would have thought they would have called me in or raised the question while I was in Jakarta, giving me some ability to respond," Jones said.