TL;DR: Tattoos are associated with organized crime in Japan.
Longer explanation: While tattoos in Japan may have originally been considered to be a status symbol and have religious importance (we have accounts of tattooed Japanese people from Chinese diplomats during the Yayoi period, 300BC-300AD), during the Kofun period (300-540AD), they became a tool used to mark criminals, coming to a head in 1720 where full-arm tattoos were used exclusively for ‘minor’ offenses instead of cutting off noses and/or ears.
All of this led to tattoos getting hugely stigmatized. Until fairly recently, the only people you could find who did have tattoos were generally part of the yakuza (Japanese mafia), who often chose hugely elaborate tattoos based off of traditional Japanese art. Here’s a few of them:
Tattoos in Japan are still so controversial that in 2012, the then-mayor of Osaka, Toru Hashimoto, launched a campaign to get companies to get rid of their employees who had visible tattoos that was very well-received, with many companies siding with him.
Many swimming pools and onsen still ban tattooed people for all of this. During the 2019 rugby championship in Japan, the government effectively begged the foreign players and supporters to please cover up in public because people will react badly, and with the 2020 Olympics in Japan, apparently the government has tried to launch an awareness campaign amongst the public that tattoos on foreigners aren’t considered a sign of criminal conduct in their home countries, because the press backlash would be a nightmare.