Tattoos, nowadays, are so common that we barely notice them anymore. However, In Japan- there is definitely a stigma associated with them. This is due mainly to their heavy affiliation with a group of people that is often referred to as "The Japanese Mafia"- The Yakuza.
Because the Yakuza are widely known across Japan as violent and dangerous (although there is tons of evidence that says otherwise- when the tsunami hit in 2011, the Yakuza were some of the first to jump to the most affected areas to provide relief) and also happen to be heavily tattooed with traditional Japanese irezumi- tattoos have become extremely looked down upon in Japan. This is super unfortunate, because with tattoos becoming more and more popular each day and with a majority of those tattoos having zero association with gang violence- it's extremely unfair to treat them as if they do.
In a recent study, it was found that 56% of hotels and inns in Japan do not allow tattooed patrons into their public baths. This has- understandably so- angered many tourists who have traveled very far to experience Japan, and been denied the ability to fully do so.
That being said, the Japanese Tourism Board is now fighting against these unfair "laws." A representative for the board, Shogo Akamichi, is hoping that a change is made very soon so that tourists are able to fully experience Japan.
As awesome as this proposal is- the catch is: This- request does not extend to Japanese patrons with tattoos.. who are still feared considerably due to possible Yakuza association.
Sigh. Baby steps.