The men were arrested in separate locations just outside Bandung city on Java island in the early hours, police said.
The arrests take to seven the number of people detained over the May 24 assault, the deadliest in Indonesia since a gun and suicide bombing attack in January last year in downtown Jakarta that left four assailants and four civilians dead.
The Islamic State (IS) group claimed responsibility for the bus station attack in the world's most populous Muslim- majority country and police have blamed local IS-linked group, Jamaah Ansharut Daulah.
"They led a meeting and gave instructions to the Kampung Melayu bombers," added national police spokesman Martinus Sitompul.
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During a raid on the suspects' houses, police found an Islamic State group flag.
The suicide attackers detonated bombs in a street outside the terminal late at night. Three police officers were killed, while six other policemen and five civilians were injured in the assault, which left body parts and glass strewn across the road in a working-class district.