They had already been taken into custody in several cities in the country at the beginning of the month, the Indonesian magazine "Tempo" reported on Friday.
A spokesperson for the anti-terrorism unit Densus 88 confirmed the information.
According to the report, the suspects are said to have published threats against the Pope on the internet.
There is also talk of contacts with the Islamist terror scene.
The investigation is still ongoing, it said.
Pope and imam sign declaration against violence
Francis has been in Indonesia since Tuesday.
On Friday morning (local time), he travelled to Papua New Guinea.
East Timor and Singapore will follow later as further stops on his Asia-Pacific trip. He is expected back in Rome on 13 September.
A highlight of Francis' visit to Indonesia was a meeting with the Grand Imam of the Istiqlal Mosque in Jakarta on Thursday.
The two religious leaders signed a joint declaration against violence and environmental destruction.