are you married?? and applying for PR? if so, are you going to Japan with your husband??
I went to south america while I was applying for PR. It was before I received the frist letter. I went there with my husband and we carried a copy of marrige license, and I had a visiter visa for another 5or 6 months, so I had no problem at all to come back to Canada!
anyway, I think you should extend your visa frist as other person said.