A caricature of the Israeli Prime Minister that appeared in Munich's Sueddeutsche Zeitung portrayed him with oversized lips, ears and nose.
The image depicted Netanyahu dressed as Netta Barzilai, the Israeli singer who won the Eurovision song contest earlier this week.
He told the Bild newspaper on Thursday that Tuesday's cartoon recalled 'the intolerable depictions of Nazi propaganda'.
The offending cartoon showed Netanyahu posing as Eurovision victor Netta, who sang for Israel, while holding a missile marked with the Star of David.
Felix Klein, who was appointed this year amid concerns over rising anti-Semitism in the country, told the Bild newspaper on Thursday that Tuesday's cartoon in Munich's Sueddeutsche Zeitung, published after the United States moved its embassy in Israel to Jerusalem, recalled "the intolerable depictions of Nazi propaganda".
Sueddeutsche, Editor-in-chief Wolfgang Krach initially said on Wednesday that Hanitzsch had indicated he merely wanted to point out that the next Eurovision finals in 2019 would take place in Jerusalem.
"Its publication was for this reason a mistake for which we ask forgiveness".
The cartoon received criticism from several high-profile German and Jewish community leaders.
"Can Israel enjoy its successful participation in a music competition without being demonized?" she wrote in an open later published on Facebook.
More than 60 protesters were killed amid fury over the opening of a new United States embassy in Jerusalem.
One of Germany's top daily newspapers has pulled a cartoon and apologised for its use of anti-Semitic stereotypes. According to the New Yorker, the newspaper was the first in the country to receive a license from the USA military administration established in Bavaria.
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