I don't believe that Himeno is correct, as it relates to Egypt. It was never a question of higher point of sale, country of residence for the card, etc. It was an unexpected devaluation of the Egyptian currency that caused the AA and OW to suspend or not file fares for trips originating in Egypt.
I had booked a DONE4 online that originated in JNB. Since LATAM issued the ticket, they had no problem converting the lower ZAR price to US $ and charging my US credit card. So, I would say to have your Japanese travel agent try again. There should be no issues with credit card residency. Forget the online booking tool. It was 'enhanced' as the BA FT'ers say.