Central Japan Railway Company says it has found a second case of improper maintenance practices involving Japan Railways Group firms.
The railway operator said on Saturday that workers had applied higher-than-recommended pressure to 11 axles when installing wheels.
The company says the axles pose no danger, but pulled the trains with them out of service anyway.
This led to reduced services on some local lines on Saturday.
The company says no data have been altered. It also says there is no guideline to follow when axles have been subjected to pressure slightly above the norm.
The cases were discovered during an emergency check ordered by the transport ministry after Japan Freight Railway Company acknowledged it had falsified maintenance data.
Central Japan Railway Company apologized to passengers for the inconvenience caused, and said it will keep working to ensure the safe operations of trains.