Officers caught the first suspect, a man in his 40s accused of pimping out boys on his Facebook page, on Tuesday in a hotel room in Cisarua on Java island.
The man, whose identity was not disclosed, was with seven boys and an 18-year-old when he was arrested, said senior police officer Agung Setya.
Two more suspects were detained on Wednesday, one who allegedly also offered boys over social media, and another accused of using the service which involved boys between 12 and 18 years of age.
“They all know each other, they’re a syndicate,” said Setya.
Investigators found 99 boys offered online at prices ranging from 1.2 million rupiah to 10 million rupiah ($90 to $750).
The police began monitoring the first suspect in August, when they came across his Facebook account during a regular online check.
He had been released from jail in March after serving a sentence for prostitution involving girls, Setya added.
Asrorun Niam Sholeh, head of the government-backed rights group the National Commission for Child Protection, urged the state to swiftly issue new laws to combat sexual crimes against children.
“We have to use this as momentum to really wage a war against sexual crime,” he said, adding that children were being “physically and psychologically damaged”.
resident Joko Widodo in May introduced tough new punishments for child sex offenders, including a maximum penalty of death and chemical castration, after the brutal gang-rape and murder of a schoolgirl sparked nationwide outrage.