The Firearms and Swords Control Law, Article 23 must be adhered to. Failure to do so will result in hefty fines. The Japanese authorities are very strict when it comes weapons seizures. They take it very seriously. However, if you have a sword and are not sure of its authenticity you should get it appraised as soon as possible.
You must bring the sword to the police station in person. Call first and let them know you will be caring it because it is against the law to carry a sword in Japan. Next, you will be asked a series of questions about where the sword was made, when it was purchased, and so on and so forth. You will receive some kind of documentation after this. Keep it and take it with you to the examination.
After that, you have to apply for registration with the Board of Education, yes that right, the Board of Education. ( kyoiku iinkai) of the prefecture where you reside. You will then be given information about when and where the registration examination will take place. Most likely at a police station. Bring the documentation that was given to you by the police, along with the sword and the registration fee. 6300 yen is what it used to cost. You may want to verify this with your own police department.
The examination is to determine whether or not the sword has any value whatsoever as an antique or a work of art. The sword has to be made in the time honored tradition of sword making. If it is not then it cannot be registered! If it is authentic you will receive a certificate of registration and from there you need to keep this registration with the sword whenever you transit with it.
If it changes ownership you need make sure to follow the same procedures for registration.