JAL executives told reporters 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.
After a second breath test before takeoff showed that he had consumed "excessive alcohol", the co-pilot was arrested by British police and required to undergo a blood test which confirmed those results, the company said in a press release.
"We are certain (the in-house breath test) wasn't conducted properly," Muneaki Kitahara, JAL's head of communications, told a press conference.
The plane departed London after a delay of one hour and 9 minutes.
"The company sincerely apologizes to the passengers and to all affected by the employee's actions," JAL said in the press release.
The incident comes only a day after All Nippon Airways revealed a hung-over pilot had caused multiple flight delays.
The male pilot in his 40s called in sick after a night of drinking on the remote resort island of Ishigaki in southern Okinawa prefecture, the company said.
The last-minute sickie forced the airline to delay five flights linking Okinawa island and smaller regional islands, affecting 619 passengers.
Following the two incidents, the transport ministry urged airline companies to strictly comply with rules on drinking.