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Jemaah Islamiah's stated aim is to build an Islamic caliphate in Southeast Asia.
Zulkarnaen, one of the commanders of the Bali attack, was arrested on Thursday by anti-terrorism police, spokesman Ahmad Ramadhan said in a statement on Saturday.
He said the officers met no resistance.
Reuters was unable to reach Zulkarnaen or find out whether he had any legal representation. According to a UN Security Council report, he also goes by the name Aris Sumarsono.
Zulkarnaen is believed to have been involved in making the bombs that were used in the Bali attacks and in the 2003 bombing of the JW Marriott hotel in Jakarta that killed 12 people.
Jemaah Islamiah's former leader Para Wijayanto was arrested in 2019.
Stanislaus Riyanta, a security analyst, said that Zulkarnaen's arrest could either weaken Jemaah Islamiah's operations or "spur them into action to prove their existence or seek revenge."
Reuters has issued a correction to this story: Corrects paragraph 6 to the 2003 JW Marriot bombing, which killed 12 people, not the 2009 JW Marriott and Ritz-Carlton bombings