Will a masters degree from Japan be seen as less valuable?
I think your decision should be based on future aspirations. Specifically, you need to decide if you are heading into industry or academia when you complete your studies. If you are going into industry, companies want people who know their stuff and can actually do something. It is the application of theory through making it tangible and not necessarily the knowledge of theory that is most valued. Studying in Japan should not injury you in this regard. Having overseas experience is yet another benefit to many companies seeking employees, especially in a country that is a leader in this field. 

If you decide to go into academia the advice of your professor is probably wisest to abide by. Exceptions to this would be if you choose to stay in Japan, which would not hurt with a Japanese degree or if you complete a PhD somewhere, which would help to overcome a master degree that some may see as "second rate."Explaining your reason for going to Japan in the admission process should mollify many PhD admission committees