Their first concern was bicycle registration. As all bicycles in Japan are registered and being caught on a unregistered bicycle could at the very least take a few hours out of your schedule, and at worst could earn you a fine. What is a bicycle tourist to do when they bring a bike with them from overseas for a short tour?
Firstly I believe its unlikely that you will be stopped by a policeman for a random registration check as you ride your fully laden touring bike around the Japanese countryside. But on the off chance that you are, simply explaining your situation should get you off the hook with a pleasant wave and a smile. If the officer is more of a by the book type then I suggest you show him your passport, itinerary, and return tickets etc. Explain there is no way to register your bike as a non-resident of Japan and you should set right to go.
What if that isn't enough? Have a picture or two of you and your bike on other trips in other countries on hand. An old Polaroid with the date in the corner adds further evidence to support the case that it is in fact your bicycle.
At the end of the day I think bicycle registration is a non issue for the short term visitor.
Their second and bigger concern was that riding of tandems is deemed illegal all over Japan with the exception of Nagano. Surely that would put a stop to their plans?
Japan does outlaw the practice of futari-nori, or two people per bicycle, but this law was put in place to stop the dangerous practice of giving your friend a lift home on the luggage rack or handlebars of a bicycle clearly designed for a single rider. As that law was being written I'm certain nobody was even considering the case of tandems. But the law is the law and two people per bicycle is specifically banned, well in writing at least.
I've heard numerous stories, and read many a blog about tandem riders all over Japan, not just in Nagano. I have even heard of tandem riders approaching policemen to ask for directions with no ill effects. I believe the police are sensitive to two people on a bicycle built for one, but when a tandem rolls by it probably doesn't even register in their minds that something is amiss as a tandem is specifically built for two riders.
As with all bicycle laws in Japan the law around tandems is fuzzy. Yes its against the law, as is riding on certain sidewalks, riding with an umbrella, and slinging a bag of groceries over your handlebars, but those laws are ignored by the populace on a daily basis and are rarely, if ever, enforced. If you're on a tandem, obeying common sense rules of the road and not putting yourself on anyone else in danger then you're unlikely to run into trouble with the law, but nothing is certain.
So, can you ride your tandem in Japan? The law clearly states two people per bicycle is unacceptable, despite being drafted without tandems in mind, so technically you shouldn't be considering bringing a tandem to Japan. But all technicalities of the law aside, others have and continue to ride tandems around Japan in full view of the local constabulary without any ill effect.
When you're riding a tandem in Japan you're bending the already quite flexible cycling rules, how comfortable you are in bending the rules will ultimately determine if you'll risk riding a tandem in Japan or not.
If you'd like a fully legal run on a tandem bicycle in Tokyo, you can borrow one for free at the Imperial Palace Cycling Course between 10:00am and 3:00pm each Sunday.