There are no special toilet facilities for assistance dogs. Assistance dogs authorised by a designated organisation under the Assistance Dogs for Persons with Disabilities Act can use the same toilet stalls as visitors. Please prepare puppy pads or a toileting harness etc. for your dog to use and ensure they are trained to use it.
If an assistance dog from overseas is recognised as meeting Japanese standards through training by an authorised overseas training provider, a "limited time certificate" will be issued by the Japanese accreditation body to ensure peace of mind during the dog's stay in Japan, and ensure the dog will be treated as a similar assistance dog.

For more information, see the Ministry of Health, Labour and Welfare website.