The transport ministry conducted an on-site inspection of the headquarters of Honda and Mazda on Monday as part of investigations into vehicle test fraud involving five vehicle makers.
The ministry last week searched the head offices of Toyota, Yamaha and Suzuki after disclosing irregularities on the part of the five companies in tests to obtain type approval, which is necessary for mass production.
The ministry is investigating details of the irregularities and examining whether there was any other wrongdoing.
After completing its investigations, the ministry plans to test 38 affected models to confirm whether they meet standards for type approval.
The ministry is set to lift its shipment suspension order for six models from Toyota, Mazda and Yamaha if they are found to meet the standards.
Honda's testing irregularities, including fraud with regard to noise testing, affected 22 models, including the Fit, all of which are no longer in production.
At Mazda, five models were affected by irregularities, including the use of doctored software in engine tests. The automaker suspended production and shipments of the Roadster RF and Mazda2.
In February, the ministry instructed 85 manufacturers and importers that had obtained type approval for vehicles and related parts to report any misconduct over the past 10 years after test fraud came to light at Daihatsu and Toyota Industries last year.
In response, the five companies reported irregularities in the tests to obtain type approval as of the end of May.