Government officials are conducting an onsite inspection at Toyota Motor headquarters in Aichi Prefecture, central Japan.
The probe follows admissions by the company and four other Japanese manufacturers that they falsified performance tests to obtain certifications for their products.
The transport ministry's inspection launched on Tuesday is based on the road trucking vehicle law. It is trying to determine what test data was falsified and the related in-house rules.
Inspectors are also interviewing executives and other personnel.
Toyota confirmed it falsified data on vehicle tests that simulated collisions with pedestrians. The tests concerned three models currently in production.
The carmaker says it also rigged the construction of vehicles used in crash tests. This involved four models no longer in production.
The other vehicle makers that have admitted to misconduct are Mazda, Yamaha, Honda, and Suzuki. The ministry says it will conduct onsite inspections at those companies as well.
Editorial note: In our initial article, we wrote, "Toyota has confirmed that it falsified data related to head injuries sustained by pedestrians in collisions." We changed the sentence to make clear the data was based on test simulations and not actual accidents.