Mr Kalifat said it was "an insult" that a French president could honour Petain on "the same level as the other generals", but he acknowledged the marshal's pivotal role in the Great War that earned him the nickname "Lion of Verdun".
"I consider it entirely legitimate that we pay homage to the marshals who led our army to victory", Macron said.
"He was a great soldier, it's a fact, he added, though he stressed that Petain had made "disastrous choices" during World War II".
The French presidency later said that only the five top military chiefs who are interred in the Invalides will be individually honoured and have their names cited in the ceremony - not including Petain. "I would urge President Macron not to offer excuse or defense for the Nazis and their supporters - in the past, present, or future".
Petain led the French army to victory in Verdun in 1916, but gained infamy and a conviction for treason for his actions as leader of Vichy France from 1940 to 1944. Yet, that would change dramatically two decades later when Petain collaborated with Nazi Germany.
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"It is shocking that France can pay tribute to a man deemed unworthy of being French in a trial held in the name of the people", said Francis Kalifat, president of Crif, the body that represents France's 400,000-strong Jewish community. But his reputation was shredded when he established the collaborationist Vichy government of unoccupied France that deported more than 70,000 Jews to Nazi death camps. "It judges the enormous and unworthy responsibility of a marshal who deliberately used his name and prestige as a cover for treason and the collaboration and deportation of thousands of Jews in France". "Petain signed the [law on] the status of Jews that meant that Jews were excluded from public function, education and forced to wear the Jewish star".
Jean-Luc Melenchon, head of the hard-left France Insoumise (France Unbowed) party, wrote on Twitter: "Marshal Joffre was the military victor of the 1914-18 war".
"Every aggression perpetrated against one of our citizens because they are Jewish echoes like the breaking of new crystal", the French prime minister wrote on Facebook, referring to the start of the Nazi drive to wipe out Jews on November 9, 1938, also known as the Night of Broken Glass. He quoted Gen. Charles de Gaulle, leader of the Free French forces in World War II and the nation's universal hero, as saying of Petain in 1966 that "the glory he earned in Verdun. can be neither contested nor go unrecognized by the nation".
Later in the day, Macron, Merkel and UN General Secretary Antonio Gutteres will join other world leaders and representatives of civil society, for a peace forum held in the northeast of Paris.
After the war's end he was arrested for treason and given the death sentence, which was commuted to life imprisonment given his age.