Japan has the most efficient, fastest and best train system in the world, so you reach by train for a daytrip also Osaka and Nagoya to vist the Zoos there.
But be warned-don't expect to see world-class zoos with western standards in animal welfare..japanese Zoos are, with the exception of Tama-Zoo and Zoorasia, far away from that. Most of them are in the standard of the 1950ty years.
But despite this fact, you will see in every Zoo in Japan species you've never seen before, of course japanese animals, but also a lot of other asian species-birds, mammals and huge"collections"of reptiles and amphibians.
The Nagoya Zoo is one the worst zoos I've been to in my life, but it has the largest animal inventory with the most species in Japan,so you you should be think about going there, if you are intersted in that. As a said, you can reach it for a day-trip by train very easy and comforbale. All large Cities in Japan do have an excellent public transport sytstem, what are always signed in english, so you will find the way to the zoos also very quick. But you can ask the poeple-the youngers ones spek englisha nd the japanese pepple are extreme friendly and helpful.
You can reach also Kobe and Kyoto Zoo by train, but both are poor, too, and not very recommended.But you have to visit Tama-Zoo in the suburbs of Tokyo, it is the largets zoo in japan with the only Mole and Shrew house in the world, the largest insectarium and butterfly hall in the world .
You also have to got to Yokohama, the neighbour city of Tokyo to vist Zoorasia-it is defenitely the"best"Zoo in Japan and keeps,for example, Proboscis monkey and Douc Langurs-and the last mongolian wild ass outside of china. There are two more zoos in Yokohama-Kanazwa-not too band, a good zoo for hoofstock lovers,( the only pronghorn outside of Northamerica), serow, goral, anoa, gaur, two rhino species,to name just a few.The last zoo in Yokohama is a desaster-Nogeyama Zoo, but the entree is free.
Toky itselfs has three Zoos-Uneo,-Tama and Inokashiarapark Zoo and five aquariums. Japn is defenitely the country for aquariums, not for zoos. Don't miss Toky Sealife Park, Kayiukan Aquarium Osaka and Nagoya Aquarium-at Hakeijima Seapaardise in Yokohama you can see whale sharks and a huge deolphinarium, Nagoya Aquariums keeps orca whales. If you wnat to see more whales, dolphins and a great"collection" of seals, some species you nevers een before-I promise, so you have to go to Kamogawa Seaworld, just a two hours ride by train from Tokyo.
Dont forget to buy the Japan Rail Pass before you go to Japan-you can ordre it in the web and it not available in Japan-it saves you a lot of money, if you want to use the train system. And don't forgot-most zoos and aquariums in Japan are closed for one day in the week-check it out in advance to plan your trip.
If you have time-go to Toba Aquarium-is has nine species of seals, african manatee,dugong, jacobita,seaotter and finless porpoise-it has around 1000 specie sin total, but you have to stay for a night at Toba, because you can't reach the city from tokyo for daytrip, but you need a whole day for this aquarium.
