The chairman of Yad Vashem said he believed extremist strictly Orthodox Jews were behind the vandalism, because one of the slogans was signed "world ultra-Orthodox Jewry".
Police are investigating what happened, but have not confirmed who they believe to be responsible.
"We are shocked and dazed by this callous expression of burning hatred against the Zionists and Zionism," said Yad Vashem's chairman, Avner Shalev. "This unprecedented act crosses a red line."
Fiona Hulbert, of the Council of Christians and Jews, said: "We are very distressed to see this graffiti, and want to assure everyone at Yad Vashem of our friendship and support. This shows that your work is needed today as much as it ever was."
