If it is the same lens, model number I don't think there should be any difference in price.
If the Japanese-built and Malaysian-built lenses are mixed together for worldwide distribution, then we would expect the price to be the same (even though one probably has a higher profit margin for Canon).
On the other hand, sometimes the large corporations will market the same product in different market locations, but it is built in Japan for one market and built in Malaysia for another market. Why would they do that? Because some markets have tougher standards for exceptance by consumers. Because some markets have more competition, so Canon might do some discount/promotion campaign in one market, and they can do that more effectively if they have a cheaper-cost product to begin with.