The comment comes as Japan's second-biggest automaker the same day recalled all 1.2 million passenger cars sold domestically over the past three years due to the issue.
Vehicles destined for the domestic market must undergo an additional final procedure performed by certified technicians before being registered with the transport ministry.
Uncertified technicians at Nissan included contract workers, Minister of Land, Infrastructure, Transport and Tourism Keiichi Ishii said at a regular news briefing on Friday.
"It's extremely regrettable, causing anxiety for users and shaking the foundation of the certification system," Ishii said. The ministry is working to discern whether and how widely the practice was known, he added.
The use of uncertified personnel constitutes the second major instance of misconduct involving a Japanese automaker in under two years, after Mitsubishi said it tampered with fuel economy tests of some domestic-market models.