The Indonesian identity card wikipedia entry says: Fingerprints are recorded from each compulsory ID cards are all fingers (of ten), but the data included in the chip only two fingers, the thumb and right index finger.
Since they record more information than they store on the card, this implies a biometric database.
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Biometric Update, November 28, 2012:
e-KTP obligates every citizen to have his or her fingerprints scanned, verified, and saved in a central database.