He said a group led by an extremist called Hendro Fernando had received US$97,000 from Jordan, Iraq and Turkey, adding that it planned to launch attacks against Jakarta's main airport and the national police headquarters.
Another group headed by a person identified only as 'Helmi' planned to use a car bomb to attack the Jakarta police complex in the city's main business district, and a third group targeted traffic police.
The arrest followed a series of January 14 attacks in Jakarta that killed four civilians and four attackers.
Indonesia, the world's most populous Muslim-majority country, suffered several major bomb attacks by Islamic radicals between 2000 and 2009, including the 2002 Bali bombings that killed 202 people.