"What can one say about a head of state who treats millions of members from different faith groups this way: first of all, have mental checks," Erdoğan said in a televised address.
Macron this month described Islam as a religion "in crisis" worldwide and said the government would present a bill in December to strengthen a 1905 law that officially separated church and state in France.
"If they aren't rid of this disease as soon as possible, it will collapse all of Europe from within," Erdoğan added.
"What can we say of a head of state who behaves like this to millions of members of a different faith in his country," said Erdoğan.
He asserted that European fascism had entered a new phase with attacks on the rights of Muslims, referring to a recent police raid on a mosque in Germany's capital Berlin that he had denounced on Oct. 23.
The Turkish president also accused France for being complicit in Armenia's decades-long occupation of the Nagorno-Karabakh region in Azerbaijan.
During his speech, Erdoğan underlined that Azerbaijan was retaking its land from Armenian occupation as fighting continued between the neighboring countries.
"I spoke with [Azerbaijan's president Ilham] Aliyev this morning," he said. "Now, our Azerbaijani brothers are marching towards the occupied territories. They have started to take them back."
Describing Turkey and Azerbaijan as "two states, one nation," Erdoğan said: "We'll continue to give all kinds of support to the struggle to liberate the occupied territories of Azerbaijan."