Officials say he helped set up and fund an Islamic militant training camp in Aceh, uncovered by police in February.
Mr Ba'asyir told reporters outside police headquarters in Jakarta that his arrest had been arranged by the US.
Mr Ba'asyir had previously served 26 months in jail before being cleared of involvement with Jemaah Islamiah (JI), the group behind the 2002 Bali attacks.
The 71-year-old was imprisoned for conspiracy over the bombings, in which 202 people died. However, his conviction was overturned and he was released in 2006.
He has been accused of giving spiritual leadership to JI, which has links to al-Qaeda - a claim he denies.
'Significant allegations'Mr Ba'asyir was arrested in West Java by anti-terror police but has not yet been formally charged. Under Indonesia's anti-terror laws police can question him for up to a week without filing charges.
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