The restaurant in Shinjuku Okubo posted a photo online on July 5, showing a notice on its window written in Japanese, Korea Times reported.
"Although diversity and tolerance are frequently discussed these days, we refuse to serve Chinese and Korean customers because we do not wish to work with unpleasant thoughts," the notice wrote.
The post quickly drawn public attention and garnered over 16 million views as of Tuesday.
The Okubo area where the restaurant is located is home to a large Korean community and attracts many foreign tourists.
"That's a discrimination sign. I oppose this and would never visit the restaurant," one person commented on the post.
"At least the restaurant should write it in English, how can we know if it's only in Japanese?" another wrote.
However, some Japanese nationals defended the action, arguing that there are many foreigners besides Chinese and Koreans and that the restaurant has the right to choose its customers, The Chosun Daily newspaper reported.
This is not the first time that a Japanese restaurant has suffered widespread criticism for refusing foreign tourists. In February, a hotel in Japan refused a Korean traveler because they did not understand Japanese.
Some of Tokyo's most famous tourist locations host bars and restaurants that do not allow foreigners to enter, with owners typically insisting there should be comfortable places for locals to spend their time away from tourist crowds.