JAL said the pilot is suspected of improperly clearing the alcohol check, as the airline's breath-testing equipment did not detect a problem.
Police then arrived at the scene, conducted a breath test and arrested the copilot that night when the test revealed a reading of 0.93 milligrams of alcohol per liter of breath - about 10 times the limit under British transport safety laws and regulations.
Ishii's remarks came after co-pilot Katsutoshi Jitsukawa pleaded guilty to being over the legal alcohol limit at a United Kingdom court.
JAL executives told reporters in Japan that the co-pilot cleared an in-house breath test but aroused the suspicion of a bus driver taking him to the plane from Heathrow Airport on Sunday.
Katsutoshi Jitsukawa, Japan Airlines first officer, was arrested at Heathrow Airport, London, for being under the influence of alcohol.
The flight was operated in a Boeing 777 aircraft which can hold up to 244 passengers.
Japan Airlines issued an apology, saying that safety was their utmost priority, and pledged to "implement immediate actions to prevent any future occurrence".
The limit for drivers in Britain is 80 milligrams.
The pilot later pleaded guilty before a court to being over the legal limit, and is expected to be sentenced on November 29.
The flight departed after a 69-minute delay.
And not just drunk, he was 10 times over the permissible alcohol limit for pilots.
In a separate incident, it was revealed Wednesday that a captain of an ANA Group company was unable to operate a flight due to the influence of alcohol, resulting in delays to five flights.
The last-minute sickie forced the airline to delay five flights linking Okinawa island and smaller regional islands, affecting 619 passengers.
JAL's company rules prohibit its pilots from drinking alcohol less than 12 hours before flying any planes.
The airline will now also involve airport staff in alcohol checks rather than allowing pilots to test each other, Kyodo news agency reported.