Japan Airlines and All Nippon Airways have each found more than 100 cases in which their pilots skipped pre-flight alcohol tests.
The internal probe followed a series of incidences recently where Japanese airline pilots have been barred from flights due to alcohol-related issues.
All Nippon Airways said that during the year through November 2018, their pilots skipped breath tests in 393 cases.
Some pilots explained that they were in a hurry after their flights had suddenly been changed. Other pilots said they saw breathalyzers being used by other pilots, and then forgot to take the test themselves.
Japan Airlines has found about 100 to 200 cases, in which its pilots skipped pre-flight breath tests.
The cases date back to August 2017, when the company introduced a new type of breathalyzer that allows test results to be sent to the airline's head office.
Both air carriers say they will assign somebody who is not a pilot to make sure that pilots carry out the pre-flight tests without fail.
Last month, the transport ministry inspected the offices of the 2 airlines, to investigate how they were enforcing their internal rules for pre-flight alcohol tests.
The ministry says it will take into account the latest findings in deciding what disciplinary measures to take against the airlines.