The police said the arrested suspects were linked to the Bali bombings and other bloody attacks across Southeast Asia.
National police spokesman Brigadier General Edward Aritonang, however, refused to divulge the exact number of those arrested or where they were picked up.
“We are looking into it,” he said.
Scores of Jemaah Islamiya members have been arrested across five countries in the region in recent months.
Another 30 of its members are in custody for the Bali bombings which killed 202 people last October.
But a top security official of neighboring Thailand said that one of Jemaah Islamiya’s top commanders could be hiding in Bangkok.
Hambali, an Indonesian man formally known as Riduan Isamuddin, is suspected of masterminding the Christmas eve bombing of churches in 2000 and is currently Asia’s most wanted-man.
He is also linked to the Bali bombings.
“Hambali has not been arrested yet but I believe he is hiding in Bangkok,” the Thai security official said.
Hambali is suspected to be the link between al-Qaeda and the Jemaah Islamiya.
Thailand had admitted last December that Hambali had sneaked into the kingdom briefly at an undisclosed date and that the police missed him by less than a day after surveillance detected his presence.