According to Wikipedia, citizens of Indonesia can/must have biometric passports [doesn't imply retaining biometric information].
According to wikipedia, Indonesia has a compulsory identity card.
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.
e-KTP obligates every citizen to have his or her fingerprints scanned, verified, and saved in a central database.
"We're putting out close to 8,000 cards per day. We have 18 machines running 24 hours per day, printing cards and encoding the chips." About 118 million e-KTP records of citizens are now stored in databases.