The initiative will also form the backbone of a crackdown on identity fraud by illegal immigrants, the Justice Minister said.
The hi-tech system will eventually replace the existing finger printing methods of the Garda Technical Bureau and the Tánaiste said it would make international cross-referencing of criminals easier.
The advanced technology involved will be particularly useful in helping track people on the British sex offenders register if they slip into the Republic, the Tánaiste said.
The system will take 18 months to implement with those seeking asylum at the Office of Refugee Applications and the technical bureau getting a first taste of it.
The electronic system will particularly target multiple asylum applications and will transmit prints to the Eurodac EU central database for cross-analysis.
The Tánaiste said enhanced biometric technology would play an increasingly important role in fighting crime, border management and weeding-out identity fraud.
“This technology is a key element in assisting the garda and immigration authorities to carry out their work effectively in areas such as crime detection, border management and identity validation generally.
“Allowing fingerprint data of migrants to be taken electronically will significantly enhance the integrity of our immigration system and allow the Garda National Immigration Bureau, (GNIB) in particular, to more rapidly detect and deal with cases of identity abuse.
“This is further proof of this Government’s commitment to providing both An Garda Síochána and the immigration service with the most up-to-date technology to assist in the delivery of an effective service to the State, its citizens and the wider community.
“Since INS was established in 2005, it has embarked on a series of measures to improve services across the whole spectrum of its activities and to strengthen the effectiveness of the immigration system,” Mr McDowell said.
The Tánaiste tested out the electronic system during a visit to the Irish Naturalisation Service in Dublin.
The GNIB will use the technology to capture prints at air and sea ports and to provide a mobile capture and search capability.
The Tánaiste insisted the legal basis for taking fingerprints of asylum seekers is clearly allowed under Irish and European law.
Asylum seeker rights organisations have objected to the move, saying it stigmatises people.