Ishii's remarks came after co-pilot Katsutoshi Jitsukawa pleaded guilty to being over the legal alcohol limit at a United Kingdom court.
It was revealed that the driver of a crew bus alerted police after smelling alcohol on the pilot.
Jitsukawa had nearly 189 mg of alcohol per 100 ml of blood in his system, which is nearly 10 times the permissible 20 mg for a pilot.
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.
The airline said the pilot drank two bottles of wine and five cans of beer for six hours from 6 pm the night before the flight to Tokyo's Haneda airport. He was remanded in custody and will be sentenced on 29 November at Isleworth Crown Court.
The Boeing 777 aircraft took off after a 69-minute delay.
It apologised on Thursday for the incident.
Khashoggi’s body was ‘dissolved’ after murder - Erdogan advisor
Turkey is seeking the extradition of 18 Saudi suspects detained in Saudi Arabia over the killing of Khashoggi. Saudi Arabia has faced a torrent of global condemnation over the killing of the royal insider-turned-critic.
The incident comes only a day after All Nippon Airways revealed a hung-over pilot had caused multiple flight delays.
"We are certain (the in-house breath test) wasn´t conducted properly", JAL communications chief Muneaki Kitahara told reporters.
Following the Japan Airlines incident, Japan's transport ministry issued a document directed at all Japanese airlines calling for the implementation of measures to control excessive drinking by flight crew.
"The company sincerely apologises to the passengers and to all affected by the employee's actions", JAL said in the press release.
The last-minute sickie forced the airline to delay five flights linking Okinawa island and smaller regional islands, affecting 619 passengers.
For the London-Haneda flight, the airline operates the route with three pilots aboard although the flying time is under 12 hours.
The airline will now also involve airport staff in alcohol checks rather than allowing pilots to test each other, Kyodo news agency reported.