In most of the cases there is longer layover in Japan you would have to accept on the other hand giving you great option to explore another city during your trip. In some case you may also find a flights with longer layover in Amsterdam - optionaly you may visit this beautiful city before you would be heading to Japan. If interested in this KLM promotional deal please look for flights departing till 30th of June 2015. Max stay 1 month. Promotional offer is valid for bookings made till 14th of April 2015 or until sold out. If you need to book your accommodation in Japan you may compare hotel rooms offered by various leading booking sites through this tool.
Booking samples
DE - Germany - Ishigaki from €494
EN - Germany - Ishigaki from £371
NL - Dusseldorf - Ishigaki from €526
Germany - Okinawa from €494
Germany - Hokkaido (Asahikawa) from €509
Germany - Tokyo from €427 (based on Air China)
All these airports in Germany are well connected with rest of the Europe by many low-cost carrierS. The easiest way how to compare your connection flights is thorugh Skyscanner.
Booking sample of cheap return flights from Germany to Japan (Ishigaki Island) for €494 here. In this case you would be departing from Hamburg to Ishigaki on 26th of April. Return flight from Japan back to Europe would take place on 8th of May 2015.