He said one of the new suspects was captured Friday in Jakarta, while the three others were arrested Saturday ouside the capital.
The 42-year-old Tholut became one of the most-wanted fugitives after bombmakers Noordin Top and Dulmatin were killed earlier this year in a series of raids.
Indonesia, a predominantly Muslim nation of 240 million, has battled extremists since 2002, when the al-Qaida-linked network Jemaah Islamiyah bombed two nightclubs on the resort island of Bali.