One of the big reasons for this is that there is no national Japanese team in FIFA. The game does have licensed national teams, such as the official England team, which have official jerseys and logos. Japan just isn't there.
The team is in Pro Evo and is used to promote the game (big European stars also promote the game in Japan).
Many Japanese gamers, of course, want to play as the national team or as J-League teams. Since they cannot in FIFA, buying Pro Evo is a no brainer. (Meanwhile, in the UK, FIFA 13 sells a million copies in one week.)
When asked at this year's Tokyo Game Show why Japanese teams are M.I.A. in FIFA, EA's Kaz Izumi told Kotaku, "It's a licensing thing."
So when EA had the Japan licensing for 2010 FIFA World Cup, the team appeared in the game.
According to Izumi, there's also the culture of Japan to contend with. Pro Evo is a long-standing series, and players are familiar with it. "Japanese people are loyal and stick to brands they know," Izumi said. "It's sometimes hard for them to accept Western games."
EA is definitely interested in appealing to Japanese players and features players like Keisuke Honda on the cover for the Japanese release. Izumi pointed out that FIFA does a great job of showcasing the Japanese players who play in Europe.
Both Pro Evo and FIFA are excellent soccer games. Cultural allegiances aside, if you need help on picking which one is right for you, Kotaku is here to help.