"France firmly refutes these latest allegations," said a foreign ministry statement. "The allegations from the ambassador are unacceptable."
France was "fully committed" to fighting antisemitism, the ministry added.
The foreign ministry statement said Kushner's comments went "against international law, and in particular the duty not to interfere in internal matters of states" by diplomatic personnel.
"Furthermore, they do not live up to the quality of the transatlantic relationship between France and the United States and the trust that should result between allies," it added.
The letter from Charles Kushner, dated August 25th but leaked to the media on Sunday, echoed Israel's criticism of France days earlier, which provoked a sharp response from Paris.
It comes just weeks before France is due to recognise Palestinian statehood, at a UN meeting in September.
Kushner's letter to Macron noted that Monday was "the 81st anniversary of the Allied Liberation of Paris, which ended the deportation of Jews from French soil" under Nazi German occupation.
He wrote: "I write out of deep concern over the dramatic rise of antisemitism in France and the lack of sufficient action by your government to confront it...
"In France, not a day passes without Jews assaulted in the street, synagogues or schools defaced, or Jewish-owned businesses vandalized," he added.
While "antisemitism has long scarred French life", the ambassador argued that hatred of Jews "has exploded since Hamas's barbaric assault on October 7th, 2023," which triggered the ongoing war in Gaza.
His remarks tally with those made by Israeli Prime Minister Benjamin Netanyahu, who on Tuesday accused Macron of fomenting antisemitism, saying it had "surged" in France following the French president's announcement last month that he will recognise Palestinian statehood.
Macron's Elysée office was quick to hit back at Netanyahu, calling the Israeli leader's allegation "abject" and "erroneous".
But like Netanyahu, Kushner denounced Macron's criticisms of Israel over the war in Gaza and his planned recognition of a State of Palestine. Such moves, he said, "embolden extremists, fuel violence, and endanger Jewish life in France".
"In today's world, anti-Zionism is antisemitism - plain and simple," the ambassador added.
France is home to Western Europe's largest Jewish population at around half a million people, as well as a significant Muslim community sensitive to the plight of the Palestinian people in Gaza.
Both communities have reported a spike in hate crimes since Israel's retaliatory offensive against the Palestinian militant group Hamas in the besieged coastal strip.
Macron's announcement that France would formally recognise a Palestinian state during a UN meeting in September drew a swift rebuke from Israel at the time.
With the move, France is set to join a list of nations that has grown since the start of the Gaza war nearly two years ago.
France is among at least 145 of the 193 UN members that now recognise or plan to recognise a Palestinian state, according to an AFP tally.
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