He was supposed to pilot the flight JL44 Japan Airlines (JAL) in Tokyo, but failed the test in 50 minutes before departure.
The airline said the co-pilot was arrested on Sunday at Heathrow Airport for violating British aviation law.
Despite passing a breath test at the company's office in Heathrow, the crew bus driver smelt alcohol on Jitsukawa and reported it to the airport's security personnel who contacted local police.
A test later revealed that Jitsukawa had 189mg of alcohol per 100ml of blood, almost 10 times the U.K.'s legal limit of 20 mg for pilots, according to the BBC.
The co-pilot, identified as Katsutoshi Jitsukawa, 42, was arrested by British police and required to undergo a blood test that confirmed those results.
The drink-drive limit in England is 80 milligrams.
At Uxbridge Magistrates' Court Thursday, the pilot pleaded guilty to being over the alcohol limit.
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Jitsukawa was taken into custody on November 29, appeared in court.
Speaking to the Asahi Shimbun newspaper, Japan's transport minister said the government would look into toughening regulations on alcohol consumption by pilots in the wake of the incidents.
Aircraft Boeing 777 took off after the 69-minute delay.
In a statement, the airline said: "The company sincerely apologises to the passengers and to all affected by the employee's actions".
The airline issued an apology, promising "immediate actions to prevent any future occurrence".
Japan Airlines said the flight was delayed more than an hour and had to be operated by the remaining two pilots.
Jitsukawa acknowledged he had drunk about two bottles of wine and a pitcher of beer the previous night, NHK said.
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