The 64-year-old executive’s car was found about 20 kilometers (12.4 miles) from his Sapporo home on Monday afternoon, but police have found no other trace of Nakajima himself.
Police said Nakajima failed to turn up for work on Monday. His wife filed a missing person’s report soon after. The president’s mobile phone had been turned off.
Nakajima worked on both days over the weekend and his wife had confirmed he was at home on Sunday night.
Police said JR Hokkaido had been issued with a warning by the Ministry of Land, Infrastructure, Transport and Tourism (MLIT) following a derailment and fire on a train on May 27 that left 36 injured. Nakajima was due to provide MLIT with a report on the incident on Sept. 14.