The drunk pilot failed a breath test just 50 minutes before the Japan Airlines flight to Tokyo.
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.
JAL said the flight was delayed more than one hour and had to be operated by the remaining two pilots.
Ishii's remarks came after co-pilot Katsutoshi Jitsukawa pleaded guilty to being over the legal alcohol limit at a United Kingdom court.
Tests found the 42-year-old first officer recorded 0.18 blood-alcohol reading, nearly 10 times the legal limit for a pilot and four times the amount for driving.
Jitsukawa, 42, attributed the elevated alcohol levels to a bout of serious drinking the previous night in his hotel bar and room, according to NHK.
The drink-drive limit in England, Wales and Northern Ireland is 80mg.
The limit for a pilot intending to fly is 20mg.
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"It is regrettable because (the co-pilot's drinking) could have affected the safe operation of the flight and damaged public confidence in Japanese aviation", Ishii said.
JAL said the pilot is suspected of improperly clearing the alcohol check, as the airline's breath-testing equipment did not detect a problem.
He was ordered detained until he is sentenced on Nov 29.
About two hours earlier, the co-pilot passed a breath test conducted by JAL along with two pilots.
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.
The last-minute sickie forced the airline to delay five flights linking Okinawa island and smaller regional islands, affecting 619 passengers.
The transport ministry on Thursday issued a document directing all Japanese airlines to report by end of the month measures being taken to control drinking by flight crew.
The plane departed London for Tokyo's Haneda airport after a delay of one hour and 9 minutes, forcing the airline to operate the flight with two pilots rather than the customary three.