The Japanese transport ministry said a trainee air traffic controller and a supervisor had repeatedly used wrong flight identification numbers as the planes flew towards each other.
Forty-two people were injured, some seriously, when the pilot of a Boeing 747 taking off from Tokyo nose-dived to avoid the inbound airliner.
The other plane, a DC10 which was flying to Narita airport from South Korea, was also forced to change course but none of its passengers or crew were injured.
The two controllers have been suspended following the incident south-west of Tokyo.
Wrong number
Reports said the trainee controller twice ordered the Boeing 747 (Flight 907) to descend, and told the DC-10 (Flight 958) which was descending in preparation for landing, to turn south-east.
At this point the supervisor apparently took over, telling the DC-10 to descend immediately, but she mistakenly called out Flight 957.
The pilot did not respond, thinking the controller was referring to another plane.
Only the pilots' judgment saved the two airliners from colliding, an official from the Japanese Civil Aviation Bureau of the Ministry of Land, Infrastructure and Transport was quoted as saying.
Near misses
Crowded skies have also been blamed for near misses. The air corridor where the incident occurred was one of the busiest in the country, with more than 400 flights a day.
Last year, Japanese pilots reported 500 cases where their onboard computers warned them to change course to avoid colliding with other aircraft, the Asahi newspaper said.
Most of those alarms went off as planes were changing altitude.
Warning
Asahi reported that in Wednesday's incident, the Boeing pilot received a warning signal as the air traffic controllers gave contradictory instructions.
The pilot is said to have acted after the second warning, which sounds when there is less than 25 seconds before impact.
A survey in 1998 found one in four air traffic controllers had been involved in incidents the previous year in which aircraft came dangerously close to each other.
Half of those surveyed said the near misses were due to their own mistakes.