It's unclear what this means for cars Nissan exported. Nissan produced around 560,000 vehicles in Japan last year to North America, Europe and other markets. Spokesman Nick Maxfield said there was no difference in quality between cars made in Japan for the domestic market and those made for export.
The recall is the second major misconduct incident involving a Japanese automaker in as many years, after Mitsubishi admitted in April 2016 it had falsified the fuel economy for some of its domestic market models.
Nissan, Japan's second-biggest carmaker, said it would recall 1.21 million passenger vehicles produced for the domestic market between October 2014 and September 2017.
It added all recalled vehicles would undergo re-inspections for final checks on issues including steering radius and braking and acceleration capabilities, at a cost of around 25 billion yen ($222 million).
"We must take the registration framework and procedures seriously, regardless of how busy we may be or how short-staffed we may be," CEO Hiroto Saikawa told reporters at a media conference.
"We apologize for the inconvenience caused to our customers."
Saikawa added the company was investigating how and why the inspections took place, a process expected to take around a month. A third party will participate in an internal investigation into the matter, he said.
The recall includes all of the 386,000 passenger vehicles Nissan sold in Japan in 2016. It excludes Nissan-branded mini-vehicles, which are produced by Mitsubishi Motors.
Passenger car sales in Japan account for roughly 10 percent of Nissan's global sales.
The announcement expands the scope of a problem reported last week, when Nissan initially said it would suspend the registration of 60,000 vehicles over unauthorized inspections.
"This could turn out to be a serious issue depending on whether the misconduct was intentional or a simple oversight," said Takeshi Miyao, managing director of consultancy Carnorama.
"At the very least it could have a big impact on Nissan's brand image, given that it prides itself for selling quality products."Nissan's shares fell as much as 5.3 percent to hit their lowest since April before closing down 2.7 percent. The benchmark Nikkei average stock price index ended up 0.2 percent.
Automakers must register all such vehicles with Japan's government before sale, with owners renewing the registrations of passenger vehicles every three years.
The Ministry of Land, Infrastructure and Transport said on Friday it has asked Nissan to report measures to prevent a recurrence of the issue by the end of October.