The stated goal of JEMA Islamia is to build an Islamic caliphate in Southeast Asia.
Sulkarnen, one of the commanders of the Bali attack, was arrested by anti-terrorism police on Thursday, spokesman Ahmed Ramadan said in a statement on Saturday.
He said the authorities did not face any opposition.
Reuters could not reach Zulkarnan or find out if he had any legal representation. He also goes by the name of Aris Sumerzano, according to a UN Security Council report.
Sulkernen is believed to have been involved in making the bombs used in the Bali attacks and the 2009 bombings of the JW Marriott and Ritz-Carlton hotels in Jakarta.
Former Jamaat-e-Islami leader Bara Vijayanto was arrested in 2019.
Security analyst Stanislas Ryanda said Zulkarnan’s arrest could weaken JEMA Islamia’s operations or “provoke them to prove their existence or seek revenge.”