If your partner is using UTF-8 or UTF-16 encoding when they send the documents, you should be able to handle Japanese automatically. But in your code, make sure to parse it as proper encoding through out the system.
If your partner is using other Japanese-specific encoding, you need to convert them to UTF-8 in the entry service, then the rest should be the same.
HTH,
#Integration-Server-and-ESB#Flow-and-Java-services#webMethods