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The firm said it would restart production at all plants except one in Kyoto from Tuesday.
"Nissan regrets any inconvenience and concern this has caused to its valued customers and other stakeholders in Japan," the firm said in a statement.
In October, the firm said it was suspending all production destined for the local market as it grappled with an inspection scandal that saw it recall some 1.2 million vehicles.
The company had admitted that staff without proper authorisation conducted final inspections on some vehicles intended for the domestic market before they were shipped to dealers.
Nissan produced 1.015 million vehicles in Japan in its last fiscal year to March, with about 400,000 units sold locally.
The scandal made a large dent in its car sales last month, plummeting more than 55 percent year-on-year.
"Nissan has taken preventive measures aimed to ensure final vehicle inspection conforms with Japanese regulations," the company said.