Katsutoshi Jitsukawa, 42, who works for Japan Airlines, pleaded guilty to exceeding the alcohol limit at Uxbridge Magistrates' Court on Thursday.
Japan Airlines said on Thursday one of its pilots was arrested by British police for drinking alcohol before a flight from London to Tokyo, leaving the airline to operate the flight with two pilots rather than the usual three.
JAL said pilot drank two bottles of wine and five cans of beer for six hours from 6 p.m. the night before the flight to Tokyo's Haneda airport.
Jitsukawa was due to be in the cockpit of the Boeing 777 aircraft that holds up to 244 passengers.
The apology came a day after another major Japanese airline, All Nippon Airways, apologized for causing delays to five domestic flights after a pilot became unwell due to heavy drinking the night before.
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. He is being held in custody and will be sentenced on November 29.
'We are certain (the in-house breath test) wasn't conducted properly, ' Muneaki Kitahara, JAL's head of communications, told a press conference.
For the London-Haneda flight, the airline operates the route with three pilots on board although the flying time is under 12 hours.
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.
In a statement JAL said: "The Company does not condone the individual's actions, as safety remains our utmost priority".
But Australia's Civil Aviation Safety Authority in the 2017-18 financial year carried out 12,130 drug and alcohol tests and got just eight positive results.
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.