WEB水族館|全国の水族館ガイド116施設
This is a website of the Aquariums of Japan. It is entirely in Japanese
kanji script (so I have no idea how comprehensive or current it is).
The link above will take you to the page listing the Aquariums of Japan. The word next to each blue dot is the region - e.g. Hokkaido, Honshu, etc - and the Aquariums are listed beneath each heading. Clicking on an Aquarium name will take you to a page describing that facility, and on that page there will be links to photos on a sister-site (a blog).
At the top left of the Aquarium Listings page (under the banner) there are two coloured bars. The top one will take you to a page for species held in Japanese Aquariums, albeit restricted to certain groups. See below for a description of how to use it. (When you go to that page, the top bar will then be for the page I discussed above, listing the Aquariums). The bottom bar relates to transport and is not important.
This is the page where you can find species in Japanese Aquariums:
水族館動物写真図鑑|WEB水族館
Not all of the following sections are searchable, but the first section is for marine mammals (in order: cetaceans, sirenians, pinnipeds, otters, polar bears, beavers). The second is for birds (penguins, waterfowl, etc). The third is for reptiles (turtles and snakes). The fourth is for amphibians (frogs and salamanders). The fifth is for marine fish (including sharks). The sixth is for freshwater fish. The seventh is for aquatic invertebrates. The eighth is for deepsea animals (fish and invertebrates).
There are clickable links for only some of these groups (in order from the top: cetaceans, pinnipeds [further separated into walrus, eared seals, and earless seals], sea otters, penguins, and sharks). However, for all of those that are there, clicking on the link will take you to a page with a photo of each species. Clicking on the link for a photo will give you a list of Aquariums holding that species.