Sorry, I replied too fast! You will have to pay the duty, uh, if they are found on you. They need to be packaged with that little seal thingie that says duty has been paid somewhere.
Really? I put all of my cigarettes (not in packs) in a tupperware type container to save them from being squashed. I know that my bags have been searched at some point between YYZ and MBJ, pretty well every year, never had a problem! Lucky I guess!