Indonesia hopes to began issuing the passports next year, Director-General of Immigration Iman Santoso told reporters at a meeting of Asia and European immigration officials on the tourist island of Bali.
The United States and Canada have already introduced such passports, which have an embedded microchip that stores a digital photo of the holder's face and their fingerprints.
"The biometric system is one way to counter terrorism and transnational crime," Indonesian Minister of Justice and Human Rights Hamid Awaluddin said in his opening speech to delegates at the two-day conference.
Santoso said the 38 countries attending the meeting plan to "fully adopt the biometric system by 2010."
Indonesia is in the front lines of the U.S.-led war on terror.
Bali has twice been the target of terrorist attacks blamed on the al-Qaeda-linked Southeast Asian militant group Jamaah Islamiyah. Suicide bombings in 2002 and 2005 together killed 222 people, many of them foreign tourists.