On September 11, 2024, a safety audit was conducted on Japan Freight Railway Company (JR Freight). The audit revealed that the company was obstructing transportation safety as specified in the attached 'Measures to Ensure Safety of JR Freight.' Based on Article 23, Paragraph 1 of the Railway Business Act, a business improvement order was issued, requiring the company to promptly implement the measures listed in attachment 3 and report the actions taken by the deadline specified in attachment 4. If the company objects to this order, it may file an objection with the Minister of Land, Infrastructure, Transport and Tourism within 60 days from the day after it becomes aware of the order. The order was issued by the Railway Bureau.

On August 30-31, 2022, the Shikoku Transport Bureau conducted a safety audit of Japan Freight Railway Company (JR Freight). The audit revealed that some electrical equipment's regular inspections, including inspection tasks delegated to other railway operators, were either not performed or exceeded the allowable inspection period. This indicates that the regular inspection and management of electrical equipment were not properly maintained. The bureau has instructed JR Freight to ensure that all electrical equipment requiring regular inspections are properly inspected and that the results are appropriately managed. The company must also establish and implement methods and systems for the execution and management of these inspections. The company is required to report on the measures taken by November 7, 2022.

On December 28, 2021, Japan Freight Railway Company (JR Freight) caused a train derailment between Senno Station and Hachihonmatsu Station on the Sanyo Line. The cause is under investigation by the Transport Safety Board. Post-accident reports indicated that the container cargo loaded on the derailed freight car was unevenly distributed (偏積), leading to the static wheel load ratio exceeding permissible limits. Additionally, the train driver did not perform train protection or roll-over prevention procedures during the incident. An audit conducted on January 24-26, 2022, identified necessary improvements in cargo loading procedures, safety management, and operational practices. JR Freight was instructed to verify the appropriateness of operational methods, conduct root cause analyses, implement preventive measures, and ensure safety procedures are properly followed. The company was also required to report on the corrective actions by May 31, 2022. Specific issues addressed include: 1) Prevention of cargo uneven loading through guidelines dissemination, staff training, and operational controls; 2) Investigation and prevention of cargo unevenness; 3) Verification of cargo loading practices; 4) Driver training and safety awareness; 5) Proper sharing of operational regulations among relevant companies; 6) Effective train protection procedures, including the use of radio-based train protection systems and signals. The guidance aims to prevent recurrence by strengthening operational oversight, staff education, and safety protocols.

Between July 13 and July 15, 2021, the Japan Freight Railway Company underwent a safety audit conducted by the Hokkaido Transport Bureau. The audit revealed that some records of track displacement inspections on sidings were not created or stored properly, violating the Railway Equipment Standards Article 114. The company was instructed to take necessary corrective actions to ensure proper record-keeping and management of track displacement inspections, including reviewing and possibly revising its inspection management system. The company was also required to report the measures implemented by September 6, 2021.