The system can judge whether passport photos match images of travelers taken by cameras at the gates in about 10 seconds, the ministry said Friday.
The system will kick off Wednesday with three gates for Japanese nationals returning home.
The ministry hopes to introduce the system at Narita, Chubu and Kansai international airports in fiscal 2018, expanding it to include departing Japanese nationals.
At the new gates, travelers will be required to remove hats and masks and stand in front of a mirror-like display where photos will be taken.
When the system fails to detect a match, travelers will be subject to screening by immigration officers.
The ministry hopes the development will allow resources to be shifted to the screening of non-Japanese visitors, whose ranks are on the rise.