Believe it or not, it is a sad truth that most of the onsen facilities in Japan do not allow people with tattoos but please don't get offended.  It's just because of YAKUZA (Organized Crime in Japan)... not because of you.

Japanese gangster, Yakuza are known to have characteristic irezumi (aka tattoos), and it has become a culture for many facilities to protect people from Yakuza by banning tattoos altogether.  In fact, the Japanese younger generation are quite open to tattoos similar to Western culture, but the older generations still associate tattoos with Yakuza.  

For those who have a tattoo and want to experience traditional Japanese onsen, there are some decent onsen facilities in Tokyo you can go to so don't worry!

Here is the list. 

• Pokapoka Land Takaban-no-yu

They have a bath set so you don't need to bring towel and other stuff.

Adult - ¥460
Kids - ¥180

2-2-1 Takaban, Meguro-ku, Tokyo
03-3713-1005
Close on Fridays
Access: 7 minutes walk from Gakugei Daigaku Station (Tokyu Toko line)

http://www.takaban-yu.com/

• Nippori Saitoyu

It was renewed in April 2015.  Nice and clean!

6-59-2 Higashi Nippori, Arakawa-ku, Tokyo
Closed on Fridays
Access: 3 minutes walk from JR Nippori Station

http://www.saito-yu.com/

• Mikokuyu

You can enjoy their natural hot spring right by Skytree.  It's very clean and Barrier free family onsen facility. 

Adult - ¥460

INFO

3-30-8 Ishihara, Sumida-ku, Tokyo
03-3623-1695
Closed on Mondays
Access: 12 minutes walk from Honjo-Azumabashi Station ( Asakusa line) or 2 minutes walk from Ishihara Sanchome Bus Station

http://mikokuyu.com/

• Tsuru-no-yu

100% Natural Black Onsen.

Adult - ¥460
Kids - ¥180

2-11-16 Funabori, Edogawa-ku, Tokyo
03-3689-0676
Close on Wednesdays
Access: 5 minutes walk from Funabori Station (Toei hHinjuku Line)

http://tsurunoyu.tokyo/

• Miyagiyu

Clear and no smell type of natural hot springs.  Men and women room switch around every week so you can enjoy different rooms. 

Adult - ¥460

2-18-11 Nishi Shinagawa, Shinagawa-ku Tokyo
03-3491-4856
Closed on Mondays
Access: 3 minutes walk from Shimo-shinmei Station (Tokyu Ooimachi line)

http://www.miyagiyu.co.jp/

• Daini Hinodeyu

Natural onsen in Kamata area. It's a typical old-school sento/onsen facility.

Adult - ¥ 460
Middle - ¥180
Kids - ¥ 80

6-5-17 Nishi Kamata, Ota-ku, Tokyo
03-3731-7761
Closed on Wednesdays
Access: 5 minutes walk from JR Kamata Station

http://www.hinodeyu.net/

I hope this list helps you!

- Maiko