The incident was attributed to errors made by air traffic controller (ATC) trainee Hideki Hachitani (蜂谷 秀樹, Hachitani Hideki) and trainee supervisor Yasuko Momii (籾井 康子, Momii Yasuko).

[4] JA8904's traffic collision avoidance system (TCAS) sounded 20 minutes after its departure[3] as the jet climbed towards 39,000 feet (11,887 m).

[2] The crew of Flight 907 avoided the collision by using an evasive manoeuvre once the aircraft were in visual proximity, and they passed within about 135 metres (443 ft) of each other.

Alex Turner, a passenger on Flight 907 and a student at Kadena High School, estimated that the avoidance manoeuvre lasted for two seconds.

[12] Flight 907, with the 747's cabin bearing minor damage and injuries, returned to Haneda, and made an emergency landing at 16:44.

[15] A similar recommendation was made three months later by Germany's accident investigation body (the BFU) in light of the 2002 Überlingen mid-air collision.

[17][18] The Tokyo Metropolitan Police Department and Ministry of Land, Infrastructure and Transport investigated the incident.

The prosecution argued that the two defendants neglected to provide proper separation for the two aircraft, the instructions issued were inappropriate, and that the supervisor failed to correct the trainee.

The defense argued that the lack of separation would not immediately have led to a near miss, that the instructions issued were appropriate, that the TCAS procedure was not proper, and that the Computer Navigation Fix (CNF) had faulty data.

[26] On 11 April 2008, on appeal, a higher court overturned the decision and found Hachitani and Momii guilty.

[27] The lawyers representing the controllers appealed, but the convictions were upheld on 26 October 2010, by the Supreme Court.

[28][29] The events of the incident are documented in the final season 3 episode of the Discovery Channel documentary Aircrash Confidential.