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.
He warned that continued Israeli settlement construction could threaten such negotiations and eventual peace prospects.
He said Israelis and Palestinians should be able "to live side by side within secure and recognised borders with Jerusalem as the capital".
On 16-17 July 1942, French police rounded up about 13,000 Jews, including about 4,000 children, around Paris and herded them into the Vel d'Hiv cycling stadium before they were sent to camps. Fewer than 100 survived the war.
Netanyahu, however, went public today with his opposition to the arrangement, stating that the ensuing conditions were advantageous to the Iranians who are seeking to expand their influence in the area.
Macron said France had organised it and blasted those who would seek to deny the state's role in the affair. "You clearly condemn and fight antisemitism, and you clearly condemn and fight this larger militancy that seeks to destroy our world".
Israeli diplomatic sources said that Iran is working to establish air, land and sea bases in Lebanon- a development which Jerusalem can not tolerate.
In response, Netanyahu said that the main issue between Israel and the Palestinians is the latter's lack of readiness to accept the existence of a Jewish state.
Macron is the latest French president to acknowledge his country's complicity in the Holocaust.
He did not indicate any eagerness for France to spearhead such negotiations after a fruitless French diplomatic effort early this year.
Netanyahu, who is looking to turn a new page with France after resisting attempts led past year by Macron's predecessor Francois Hollande to restart the peace process via an worldwide conference, said Israel and France shared a desire to see "a stable and peaceful Middle-East".
Pro-Palestinian and other activists protested Netanyahu's appearance in Paris, criticizing the settlements and the blockade of Gaza.
The French leader criticised Trump over his renunciation of the Paris climate accord, but he stressed their close cooperation against the Islamic State group in Syria and Iraq.