Both JAL as well as ANA, the two largest Japanese carriers now offer Halal food on all their international flights provided that you book for the Halal menu in advance. The booking can be made via telephone to their respective offices at least 24 hours before the boarding time.
To get detailed information on how their booking-by-telephone system works for getting 100% certified Halal meals while flying with these airlines, you may click on the following two links for the two airlines.
The Halal dishes are prepared in their especially designed Halal-kitchens available both in Japan and overseas. Any questions can be directed to their offices to get a more thorough understanding of how and what type of Halal foood they supply in their international flights.