The French president called on Israel and the Palestinians to renew peace talks and warned that ongoing construction of Jewish settlements threatened the region's chances for peace.
The president denounced his country's collaboration in the Holocaust, and lashed out at right-wing nationalists who still downplay the French role in the deaths of tens of thousands of Jews.
The meeting between the two leaders at Elysee palace followed a commemoration of the victims of a mass arrest of French Jews in 1942, known as Vel d'Hiv raids.
During the French presidential elections earlier this year, National Front leader Marine Le Pen said it was not France that was responsible for the roundup, but rather "those who were in power at the time".
Israeli Prime Minister Benjamin Netanyahu said he opposes the cease-fire brokered by the United States and Russian Federation in southwest Syria, near the border with northern Israel's Golan Heights. Stressing that global law should be "respected by all", Macron said, "I am thinking here of (Israel's) continued building in occupied Palestinian territory".
Mr Macron said "it was indeed France that organised this", adding "not a single German" was directly involved, but French police collaborating with the Nazis.
Macron said on Thursday that he would not tolerate public dissent from the military after General Pierre de Villiers reportedly told a parliament committee he would not let the government "fuck with" him on spending cuts.
Macron condemned the terror attack last Friday in which two Israeli police officers at the Temple Mount in Jerusalem's Old City lost their lives.
"We will never surrender to the expressions of hatred", Macron said Sunday in Paris. Netanyahu has repeatedly said Iran is a threat to the Jewish state, the Middle East and potentially the world.
"Militant Islam wants to destroy our common civilization", Netanyahu told the French president. "They seek to destroy Europe".
They also discussed the war in Syria Macron also said that he was concerned about Israel's security, a statement that might be worrying for the protesters gathered on the streets of Paris this week.
Pro-Palestinian and other activists protested Netanyahu's appearance in Paris, criticising Jewish settlement policy and the blockade of Gaza.