Jean-Francois Jalkh, who firmly rejects the allegations, is accused of making questionable remarks about the Nazi gas chambers..
According to reports, it is claimed that Jalkh, a vice-president of the party, once questioned whether the Germans used Zyklon B gas to murder Jews in Nazi concentration camps.
He is alleged to have rejected the established historical fact that Zyklon B gas was used inside gas chambers. He is also said to have endorsed the work of known Holocaust denier Robert Faurisson.
Speaking to CNN affiliate BFMTV, Le Pen said that Jalkh was "extremely affected by this defamation."
Louis Aliot, Le Pen's partner and spokesman, confirmed during an interview with BFM that Jalkh will be replaced by Steeve Briois, another party vice president.
Briois is currently facing charges of inciting racial hatred for a tweet that made a link between migrants and sexual assaults.
"Mr. Jalkh never made any revisionist statement, and it is a total lie to say otherwise. It is contrary to his personal sense of honor," Jalkh's lawyer David Dassa-Le Deist said.
The National Front has been dogged by accusations of Holocaust denial throughout the campaign.
In March, Benoit Loeuillet, a National Front regional councilor in the southern region of Provence-Alpes-Cote d'Azur, was suspended after being caught on a secret camera claiming mass murder had not taken place during the Holocaust.
Then, earlier this month, Le Pen sparked outrage by suggesting France was not responsible for the wartime round-up of Jews who were sent to Nazi death camps.
Her stance is at odds with former president Jacques Chirac and current premier Francois Hollande, who have both apologized for the role played by French police in the rounding up of 13,000 Jews at the Vel d'Hiv cycling track in Paris
, ordered by the Nazis in July 1942.
According to Yad Vashem, the Holocaust Museum
in Jerusalem, some 1,000 Jews were deported to Auschwitz every two or three days in the two months following the arrests at Vel d'Hiv. Nearly 38,000 Jews had been deported to Auschwitz from France by the end of September 1942. By 1945, just 780 of them remained alive.
Le Pen's comments were condemned by rivals, Jewish groups and the Israeli Foreign Ministry.
Le Pen has attempted to distance her party from accusations of anti-Semitism, which were prevalent under the leadership of her father, Jean-Marie Le Pen
The party's founder, he was expelled in 2015 for comments
in which he denied the Holocaust.
During his career, he referred to the gas chambers used by the Nazis to systematically murder the Jewish population as "a detail of history."
The expulsion of the party's founder by his daughter caused huge controversy and resulted in the two having a public falling out.
Le Pen has tried to move her party away from such rhetoric but this latest episode is unlikely to help such efforts.
Since stepping down as leader of the National Front on a temporary basis, Le Pen has attempted to broaden her appeal.
On Friday, she released a video on Twitter urging those who had voted for the far-left candidate Jean-Luc Mélenchon
to prevent rival Emmanuel Macron from becoming president.
Macron survived the first round of voting and enjoys a healthy lead in the polls.
"I would like to put our differences and disputes aside ... we have to fight today," she said. "We cannot let France to Emmanuel Macron. The risk is too important."