Justice Minister Eveline Widmer-Schlumpf says electronic passports will help guarantee the freedom to travel abroad and prevent abuses.
She made the statement at the start of a campaign on Monday ahead of a nationwide vote on the issue on May 17.
The biometric passports include a chip that stores two fingerprints and the holder's facial image to be kept in a central database.
Widmer-Schlumpf said such a register was reliable and efficient. She added that access to the electronic record would be limited to the passport authorities.
The new travel documents are a requirement of a European treaty that became operational in Switzerland in December 2008. It also facilitates visa-free visits to the United States, according to the justice ministry.
A group of centre-left and rightwing politicians argue it should be possible to acquire a conventional passport. They also say a central database allows the state to interfere in the private sphere of its citizens.
Opponents collected enough signatures to challenge a decision by parliament last year to a referendum.
swissinfo with agencies