Japan Freight Railway Company halted all trains on Wednesday after acknowledging it had falsified maintenance work data.
The company revealed on Tuesday that it had manipulated figures on pressure applied during wheel-to-axle fittings.
The firm said the practice started at least 10 years ago, and involved at least 564 cars.
The company said on Wednesday that it was still looking into cases involving another 300 cars.
The suspensions caused disruptions for logistics firms, delaying deliveries.
Japan Freight Railway President Inukai Shin said he offers an apology to its customers and other relevant people.
The transport ministry plans to inspect the company’s three offices that were involved in the misconduct to determine what happened and check the safety management system.