Upvote:1
Go to the check in counter in Canada: tell the check in person that you want to use your Canadian passport to leave Canada and to enter Japan, and that that you will use your US passport to enter and leave the US. The check in person will probably need to capture this in your travel records, so the info that will be sent to US and Japan will be corrected.
You may want to head to the airport a littler earlier to get this sorted out.