Will a masters degree from Japan be seen as less valuable? I'm a canadian engineering  undergraduate student in the field of robotics and I'm considering doing a masters degree in Japan when I finish my bachelors.

I've talked about this with my internship supervisor (a well known professor in my subfield) and he claimed that research in Japan is usually seen as less relevant because (his words) :


  they tend to stay isolated from the worldwide community and ignore
  new developpements from other researchers.


I'd really like to study in Japan as I have a great interest in their culture and also because popular culture suggests that Japan is one of the leading countries in the field of robotics (This might be wrong).

However, I would also like my future masters degree to not be seen as second rate.

Will a masters degree in Japan be seen as less valuable? and if so, how would it impact my future career?
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