0837 GMT November 30, 2020
Khan's condemnation follows statements Macron made last week after a French teacher was beheaded near Paris, AFP reported.
The teacher had shown cartoons of Prophet Muhammad (PBUH) during a class. Macron said the teacher "was killed because Islamists want our future".
In a series of tweets, Khan said the remark would sow division.
"This is a time when Pres Macron could have put healing touch & denied space to extremists rather than creating further polarisation & marginalisation that inevitably leads to radicalisation,” he wrote.
"It is unfortunate that he has chosen to encourage Islamophobia by attacking Islam rather than the terrorists who carry out violence."
The history teacher, Samuel Paty, had provoked outrage by showing to his students the blasphemous cartoons of Prophet Muhammad (PBUH), published by the French satirical newspaper Charlie Hebdo, according to Press TV.
He was murdered outside his school in a Paris suburb on October 16 by an 18-year-old assailant, identified as Chechen Abdullakh Anzorov, who was shot dead by police soon after the killing.
"By attacking Islam, clearly without having any understanding of it, President Macron has attacked & hurt the sentiments of millions of Muslims in Europe & across the world," Khan said.
In an address to the United Nations last month, Khan blasted Charlie Hebdo for republishing the cartoons, saying "willful provocations" should be "universally outlawed".
Several Muslim countries have called for a boycott of French goods.
Palestinian resistance groups based in the Israeli-besieged Gaza Strip also blasted Macron for defending the offensive cartoons, Press TV wrote.
In a statement released on Saturday, Hamas said, “Insulting religions and prophets is not a matter of freedom of expression, but rather promotes a culture of hatred,” warning of unspecified “consequences”.
"Macron's encouragement to publish insulting cartoons of the Prophet (PBUH) is an attempt to revive the Crusades which France was the source of its trigger," said Sami Abu Zuhri, a senior Hamas spokesman.
For its part, the Islamic Jihad stressed that "offending" Islam, and Prophet Muhammad (PBUH) is a "red line" that "could not be tolerated”.
Earlier, in a tribute to the slain teacher, the French president described him as a “quiet hero” and posthumously awarded him the Légion d'Honneur, the country’s highest civilian honor.
Macron also vowed his country would not "give up cartoons" depicting Prophet Muhammad (PBUH), claiming that Paty was killed by "cowards" for representing the secular, democratic values of the French Republic.
On Saturday night, hundreds of Arabs in Israel gathered outside the residence of French Ambassador Eric Danon in Tel Aviv’s Jaffa district to voice their anger at Macron’s comments.
The protest began after Muslim evening prayers, with the participants holding up banners written in Arabic in support of Prophet Muhammad (PBUH).
One of the demonstrators, Amin Bukhari, accused Macron of playing the game of “the extreme right”.
“The Prophet Muhammad is the most sacred figure in Islam and whoever attacks his honor, attacks an entire people,” he told the crowd. “We must respect Moses among the Jews, we must respect Jesus Christ who is our prophet too, and we must respect the Prophet Muhammad (PBUH).”
Also in the southern Gaza city of Khan Yunis, Palestinian protesters burned photos of Macron and called for the defense of both the prophet and Islam, Le Figaro reported.