"I consider it entirely legitimate that we pay homage to the marshals who led our army to victory", Macron said.
Macron's plan to honour Petain alongside seven other French marshals who directed military campaigns during World War One, which ended 100 years ago on November 11, has unleashed criticism from Jewish groups, political opponents and on social media.
"He was a great soldier, it's a fact", he said, though he stressed that Petain had made "disastrous choices" during World War II.
"I don't forgive anything but I don't erase anything from our history", he said.
The French presidency later said that only the five top military chiefs who are interred in the Invalides will be individually honored and have their names cited in the ceremony -not including Petain.
But Wednesday's remarks struck a deep chord in a nation that has lived through two world wars and only in recent decades has acknowledged its collaborationist past. His administration oversaw the deportation of over 76,000 French Jews to death camps on the Nazis behalf.
Jewish association CRIF said it was shocked by the comments. "It judges the vast 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". Chirac spoke at the Vel' d'Hiv cycling stadium in Paris, known for a 1942 roundup of French Jews that saw 13,000 people deported to Nazi concentration camps, a third of them children. "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".
After a record year in 2015, anti-Semitic acts fell by 58 percent in 2016 and went down a further 7 percent last year; however, there has been an increase in violent acts targeting Jews.
The ceremony is another symbol of reconciliation between France and Germany, as Rethondes was also the site imposed by Nazi Germany on the French when accepting their surrender in 1940 during World War II, the Elysee said.
"Petain is a traitor and an anti-Semite", tweeted Jean-Luc Melenchon of the far-left France Unbowed party, echoing a flurry of angry postings.
After the war, Petain was sentenced to death for treason, though then-President General Charles de Gaulle, a longtime admirer of Petain's military feats of arms, reduced the punishment to life in prison.
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.