Applying for a Physics Masters as an international student I am a citizen of Bangladesh, an underdeveloped country in South East Asia.

I would like to apply to universities in Canada for a Masters degree. In particular, I would love to secure an admission to York University or the University of Waterloo. However, I've learnt that students coming from the Indian sub-continent must have already done a Masters to apply for a Masters degree. How true is this?
You can pose these questions to the institution you are most interested in applying to.

I doubt you need a Masters in order to apply for a Masters.

In general, I recommend applying for a PhD.  If you decide to stop with a Masters, that's okay.  Check this with the particular institution, of course -- but in general, I think that applying for the PhD program would give you the best chance of financial support (research assistantship or teaching assistantship).