The suspects had been collecting funds for JI via two Islamic charitable foundations and their arrests will help build a picture of militant funding in Indonesia, Aswin Siregar of the Densus 88 counterterrorism force told media on Thursday.
JI is accused of orchestrating the 2002 Bali bombing of two nightclubs, which killed more than 200 people, including many Australians, and several other deadly attacks in the capital Jakarta.
Based on financial reports, police said the two foundations used as fronts for JI had raised about $2 million, although the figure could be higher.
Cash equivalent to $700,000 was discovered at the office of one of the foundations, police said.
A senior member of Indonesia's Islamic Council who was arrested earlier this month was among the 24 detained.