The flight was delayed by more than an hour.
The airline said the co-pilot was arrested on Sunday at Heathrow Airport for violating British aviation law.
A Japan Airlines pilot who was arrested shortly before a flight for being drunk had nearly 10 times the legal alcohol limit for a pilot, London police said Thursday. It will also prohibit pilots from drinking alcohol 24 hours prior to flights, compared to the current 12 hours.
Tests found the 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.
Jitsukawa admitted he had consumed more than 1.5 litres of wine and more than 1.8 litres of beer the night before, both in the hotel bar and in his bedroom, reported Japanese broadcaster NHK.
The limit for drivers in Britain is 80mg.
According to NHK, the first pre-flight test did not detect alcohol on Jitsukawa's breath.More news: Chelsea fans hail Mason Mount after his Derby performance at Stamford Bridge
The device used for the breath test requires users to breathe into its main body. The copilot breathed into a device in front of the two captains but did not test positive for alcohol, according to the airline.
The copilot joined JAL in 2000 and has worked as a pilot for about 15 years.
For London-Tokyo flights, the airline operates the route with three pilots aboard although the flying time is under 12 hours.
"We are certain (the in-house breath test) wasn't conducted properly", Muneaki Kitahara, Japan Airlines' head of communications, told a press conference. The airline said that within the month, it would start using a new detection device used at Japanese airports at all airports worldwide.
The incident came to light after All Nippon Airways Co. on Wednesday apologized for five flight delays in Okinawa last week because a pilot was not in a fit state to work following a night of drinking.
Transport Minister Keiichi Ishii on Friday told reporters that the government would look into tightening the rules on drinking by flight crews.