[Hatredcopter]

Immigration in Japan can be notoriously bad with CoE's. They say it takes 3 to 4 weeks to get it processed once they receive the paperwork from your sponsor institution, but I've heard of it taking even longer during their peak season (over two months in some cases). The good news is that once you do receive it, it only takes about 3 days for the consulate to have your visa ready. I would definitely look at your airline's terms for changing flights, just in case.

In the meantime, I'd contact your nearest consulate and ask them whether its possible to get your visa sorted after landing in Japan.