The Japan Airlines plane departed London after a delay of one hour and 9 minutes.
Japanese broadcaster NHK reported that police were alerted by the driver of a crew bus who smelled alcohol on the pilot.
Tests found the 42-year-old first officer had 189 milligrams of alcohol per 100 millilitres of blood in his system, nearly 10 times the 20mg limit for a pilot.
The drink-drive limit in England is 80 milligrams.
The Daily Mail reported that although the plane bound for Tokyo's Haneda airport was delayed by only one hour and nine minutes, the airline had to make the hard decision of flying with only two pilots, rather than the customary three.
JAL had prohibited its pilots from drinking alcohol 12 hours before getting on their flights.
The airline said Thursday that Jitsukawa, 42, had been arrested by British police for being about 10 times over the legal limit set under the U.K.'s aviation law after he drank two bottles of wine and more than 1.8 liters of beer over a period of six hours from 6 p.m. Saturday, the night before Sunday's flight. The two pilots who took the test with the co-pilot did not notice anything wrong with his behavior.
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The airline suspects the co-pilot somehow cheated on the earlier test.
When queried about his physical condition, the copilot reportedly said he felt a little sluggish.
JAL executives told reporters that Jitsukawa cleared an in-house breath test but aroused the suspicion of a bus driver taking him to the plane from Heathrow airport on Sunday.
Breath tests are not even required. "There is no doubt the copilot did not correctly measure his breath", a JAL official said.
JAL subsequently apologized for the breach and admitted that an in-house breath test was not conducted properly.
The incident is "deeply deplorable as it may undermine people's confidence in aviation security", Land, Infrastructure, Transport and Toursim Minister Keiichi Ishii said at a press conference on Friday after a Cabinet meeting.
The incident comes a day after another major Japanese airline, All Nippon Airways, apologized for causing delays to five flights after a pilot became unwell due to heavy drinking the night before.