At Uxbridge Magistrates' Court on Thursday, the pilot pleaded guilty to being over the alcohol limit.
First officer Katsutoshi Jitsukawa, 42, was arrested at the Heathrow airport after failing a breath test just 50 minutes before the flight number JL44 to Tokyo was due to take off with him as the main pilot.
Tests found the 42-year-old first officer had 189 milligrams of alcohol per 100 milliliters of blood in his system, nearly 10 times the 20 milligrams limit for a pilot.
Under Japan's Road Traffic Law, drivers are considered to be driving under the influence if they have an alcohol-per-liter-of-breath reading of 0.15 milligrams or higher.
The co-pilot acknowledged he drank about two bottles of wine and a pitcher of beer the previous night, NHK said.
He has been detained until he is sentenced on November 29.
Drinking is banned more than 12 hours before departure if it could affect one's ability to operate a flight.
JAL have apologised for the incident and said: "Steps will be taken to prevent future occurrences".
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JAL subsequently apologized for the breach and admitted that an in-house breath test was not conducted properly.
'The company sincerely apologises to the passengers and to all affected by the employee's actions, ' JAL said in the press release. The pilot was reported to have called in work sick after a night of drinking on the remote island of Ishigaki.
The limit for a pilot intending to fly is 20mg.
The last-minute sickie forced the airline to delay five flights linking Okinawa island and smaller regional islands, affecting 619 passengers.
"We will use all possible means to ensure flight safety", Ishii told reporters, adding that the government will study standards enforced by other countries in implementing stricter rules for the industry.
Following the two incidents, the transport ministry urged airline companies to strictly comply with rules on drinking.
For the London-Haneda flight, the airline operates the route with three pilots aboard although the flying time is under 12 hours.