Its a good idea to attach emergency contact information to the crate.All animals traveling oversees must have a valid health certificate and rabies certificate. These certificates are only good for 10 days so make sure your pet has a valid certificate that is properly filled out and given all the proper official stamps. If you do need to leave your pets behind with a friend or kennel until they can travel to meet you please be sure to fill out a "permission to treat" for the people that are caring for their pets so they can be taken to the veterinarian in order to receive the proper paperwork.
Right now the issue that seems to be emerging for families that have left and are working on having their pets join them is that the airlines are insisting on an intermediary to ensure proper paperwork and travel arrangements. While this will add a considerable cost to getting your pets home safely it will help get them to you. The intermediary should be someone who is knowledgeable about the procedures since you are no longer in the country as well as a native speaker. I am sure the people at the Cargo Desks at Narita Airport (Tokyo) are Japanese speaking and so it would be difficult to communicate with them for a non fluent speaker half a world away.
My suggestion is to get in touch with the Veterinarian on base and ask him if he knows of a kennel that will also drop off / pick up animals at the airport. There is a kennel like this in Hong Kong that is always helping ex-Pats from all over the world get through the paperwork and confusion. They will get the documents together and come highly recommended by all the veterinarians that ex-pats use. I would think that the same would exist in Japan. If the base Veterinarian doesn't know of anyone who offers this service try contacting a Veterinarian in an ex-pat community they should know know.
If that doesn't work out because of the current situation and disaster families that need help shipping their pets out of the country should contact a member in good standing of IPATA http://www.ipata.com/find-a-pet-shipper/search-on-line-for-a-pet-shipper/
Another option would be to contact an International Moving Company who has offices around the and see if they can help. They don't ship animals themselves but have agents that they are affiliated with who do since they help facilitate international moves for families and companies all the time. There is often a premium fee with this service but it might be one of the only options available especially in disasters for ex-pat families.
One option that exists for Military families during evacuations if they have already left is that a friend can take the pets on US Chartered Flights back to the US with them. As the pets owner you will need to sign a power of attorney over your pets to the friend so the animals can fly back to the US with them on the chartered flights. Each family is allowed 2 pets plus their regular allowed luggage. So this could be an option especially if you have a really nice friend or are in a jam because you were grandfathered into the only 2 pets per family on military bases rule and have more then 2)
If you have any special needs or concerns please let us know as we now have contact information for many organizations and their volunteers on the ground in Japan and have been working with them in order to help families. But it is best to go to them with detailed information so they can figure out how they can best help the situation. Please don't just leave your pets behind without putting some sort of plan in place.
Learn more about IPATA to see the rules and regulations their members have to follow.