More than 130 domestic flights using Tokyo's Haneda Airport are canceled on Thursday, due to the plane collision on Tuesday evening.
Around 28,000 passengers of Japan Airlines and All Nippon Airways are likely to be affected.
Japan Airlines canceled 66 domestic flights to and from Haneda.
All Nippon Airways scrapped 65 domestic flights.
Air carriers say their schedules may still change. They are advising passengers to stay updated with the latest flight information.
More than 200 domestic flights to and from Tokyo's Haneda Airport scheduled for Friday have been cancelled, due to the collision involving two planes on Tuesday evening.
Japan Airlines has canceled 102 domestic flights. All Nippon Airways has scrapped 98, and Starflyer has dropped 14. Skymark Airlines has cancelled one flight.
Air carriers say there may be further changes in their schedules. They are advising passengers to stay abreast of the latest flight information.
Services are expected to remain disrupted until all debris has been removed from the runway and safety checks have been completed.