I found this...
Which linked to this...
Which says this:
Strict regulations on importing of "Rodents",
such as Hamsters and Squirrels.
Hamsters, Guinea pigs, Squirrels and Chinchillas are
classified as “Rodents”.
Importing “Rodents” are enforced because “Rodents”
are known to have a lot of serious infectious diseases
that can be harmful to humans.
For rodents, the health certificate must verify that the
animal was kept since birth in a storage establishment
recognized by the government authorities. Rodents
raised at home will not be regarded as a recognized
storage establishment.
Importing rodent pets raised overseas or purchased
from overseas pet shops are subject to these
regulations. As health certificates issued by government
authorities may be difficult to obtain for such animals, in
general, these animals cannot be imported to Japan.
There are a few numbers in that PDF for the Quarantine Stations. I'd call them for info.