an exposure in japan few years ago. in kyoto, we were staying at a small hotel in the suburb. within walking distance from the hotel, our ang mo guide guided us through a walk in the neighbourhood. we walked past a three storey stand-alone bungalow with cadillac in the front porch. there were men in full suit hanging around. later, we were told by our guide that it was the residence of a yakuza boss.
later, at a public bath, two of us, me included, went in to have a bath. in it, we saw a few of the 'henchmen' fully unclothed, full tattoos from shoulder to ankle. they did not bother us at all.
in my view, they usually do not bother others, as they are not petty criminals.
Japanese people generally keep to themselves minding their own business. Just avoid eye contact like on a parisan subway, turn off ur handphone ringtone and for heaven's sake do not photograph the yakuza
Japan is a very safe country to travel la, of course when u are there dont do stupid things, respect their culture and have fun however as the saying goes "low crime doesnt mean no crime" just use some common sense.
I was in Tokyo, Kyoto and Osaka in early April on a group tour. Tokyo is where the Yakuza has very strong control over their territories. The guide brought us to the red-light district in the morning as an eye-opener. But he cautioned that he would not bring us anywhere near the district at night, to avoid trouble. So, just stay away from trouble and Japan is very safe.