In its report, the NTSB determined that the probable cause of the collision was "inadequate interaction and communication among senior members of the combat systems team (the commanding officer, the officer of the deck, the fire control technician, and the sonar supervisor), which resulted in the failure to perform adequate contact analysis and adhere to proper procedures for moving to periscope depth; and the commanding officer's decision to order an emergency surfacing maneuver."

Also, contributing to the cause of the accident was the "failure of the crew, in particular the commanding officer, to adequately manage the civilian visitors so that they did not impede operations, the report said, adding that contributing to the loss of life was the rapid flooding and sinking of the Ehime Maru, which occurred when the submarine's rudder tore through the fishing vessel's lower deck spaces," the report states.

The Ehime Maru was in the middle of a 74-day training voyage that had originated in Japan on Jan. 10. During the vessel's one-day stopover in Honolulu, its air conditioning system was repaired.