A clip of the comedy routine resurfaced on social media ahead of Friday’s ceremony.
According to a translation offered by the New York Times, in the clip Mr Kobayashi “joked about ‘massacring Jews’ while miming the act of cutting up human figures made of paper.”
Mr Kobayashi apologised for the “extremely inappropriate” lines in a statement to AFP.
"It was from a time when I was not able to get laughs the way I wanted, and I believe I was trying to grab people's attention in a shallow-minded way,” he said.
Japanese Prime Minister Yoshihide Suga condemned the “utterly outrageous and completely unacceptable” incident in a statement to NBC News.
The US-based Simon Wiesenthal Centre criticised the sketch.
“Any person, no matter how creative, does not have the right to mock the victims of the Nazi genocide.
“The Nazi regime also gassed Germans with disabilities.
“Any association of this person to the Tokyo Olympics would insult the memory of six million Jews and make a cruel mockery of the paralympics,” said the organisation’s associate dean and global social action director, Rabbi Abraham Cooper.
The opening ceremony takes place tomorrow at midday, UK time.
The lead up to the Tokyo Olympics has been marred by a number of scandals and criticism over the games taking place during the pandemic.
