If you are flying with JAL, feel free to let them know about your dietary restrictions. You can request a special meal by phone up to 25 hours before your departure via the JAL website, and 24 hours before your departure via phone or mail.
For ordering through the website, visit the JAL website and click the "Service Selection (Seat/Meal)" button for your flight on the Booking Details screen. Meals may be ordered on the "Optional Service" screen when booking a new ticket.
Japan Airlines In-Flight Halal Menu