The men, aged 18, 26 and 27, belong to an Orthodox group opposed to Israel's existence and admitted to the vandalism, police spokesman Micky Rosenfeld said. They were due to be arraigned in court later in the day.
Some of the graffiti, all written in Hebrew, accused Israel's founders of secretly encouraging the slaughter of six million Jews by the Nazis during World War Two to hasten the creation, in 1948, of the Jewish state.
Prime Minister Benjamin Netanyahu called the slogans outrageous and said after the incident it was hard to believe "a human being could be capable of writing such things".
Some Orthodox Jews regard modern-day Israel as an abomination, believing the establishment of a Jewish state must await the coming of the Messiah.
Yad Vashem, a museum and memorial, was established on a Jerusalem hilltop in 1953 and is often visited by foreign leaders who lay wreaths in its stark Hall of Remembrance.
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