Sartono, 34, who goes by a single-word name, said he molested 54 children in the past two years and kidnapped, molested and sold 42 others before 2008, Thousand Islands Detective Reynold E.P. Hutagalung told The Jakarta Post.
Sartono, who police alleged typically raped "street kids" he met at train stations, has denied murdering anybody, the Jakarta Globe reported.
He also denied ever being sexually abused himself as a child.
Sartono was arrested in a police sting operation at a Jakarta Old Town train station after the boy's parents contacted police.
The boy, an eighth-grader identified only as H.R.L., went missing Nov. 21 and returned home Dec. 3 claiming he had been abducted and raped, police said.
Sartono allegedly promised to take H.R.L. to mainland Jakarta from the Thousand Islands to buy him a cellphone.
"The victim claimed to have escaped from the perpetrator in Purwakarta (the capital of West Java's Purwakarta regency), then made it to Jakarta and took a ferry back home to the Thousand Islands," Thousand Islands Police Chief Hero Hendrianto Bachtiar said at a news conference.
The Indonesian Child Protection Commission will provide counseling to H.R.L., who has refused to go to school since returning home, Hero said.