National Police spokesman Sisno Adiwinoto told the Antara news agency fingerprints and "other information" led to the identification of Abu Dujana, who used at least seven other names.
Dujana and seven other terror suspects were arrested in a series of raids Saturday in central Java, the Jakarta Post reported Wednesday.
The Islamist Jemaah Islamiyah group is blamed for the deadly bombings of resorts in Bali in 2002 and other attacks, the report said.
Sisno said he wouldn't release information on the other suspects as the investigation was ongoing and further arrests were expected.
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