Yes, there's several choices on the software you can use but I recommend gnome + canna/freewnn + im-ja or kde + canna/freewnn + kinput2.
gnome with im-ja is easier to configure, basically just install canna/freewnn(doesnt matter which one), make sure they are started, install im-ja
configure it by invoking "im-ja-conf"
After thats done you'll be able to use it in any gtk apps just by right click then select input method-japanese.
For kinput2 you have to somehow make it start when X starts for invoking kinput2& manually.