Hi. In June Im flying from Europe to Japan with my bike and am facing the same problem. I've done a lot of research on that matter and decided to pack my bicycle (an European Koga-Miyata, very similar to yours 1000 if not identical) in a huge carton box. This way you can pack it up with extra rugs or carton pieces to protect the frame and components and I have a feeling this will work better then just putting the bike into a bag. When you land you can easily dispose the box, and when you fly back just check local bike stores for a box.

Hope this helps.

PS. There are also dedicated hard-shell bike boxes, but those are quiet expensive and there's really nothing to do with it once you land and unpack your bike.