My understanding while talking to people there is that the Japanese are starting to view tattoos on foreigners differently than on Japanese. You have to consider that in the past criminals were tattooed in Japan, which is how the Yakuza began, and tattoos have only recently become acceptable in North America and Europe. My generation is probably the last that views clean, clear skin as beautiful.
If you stick to the larger cities and cover up the ink as best as you can, then you’ll likely be okay. But if you travel to the countryside, and plan to visit onsen and sento, then expect to be barred. Watch for the signs (one is shown below) and show your respect for the country by accepting their opinion of ink.