He said Mr Macron needed a mental health check for pledging to defend secular values and fight radical Islam.
Mr Macron has spoken out forcefully on these issues after a French teacher was murdered for showing cartoons of the Prophet Muhammad in class.
Depictions of the Prophet Muhammad can cause serious offence to Muslims because Islamic tradition explicitly forbids images of Muhammad and Allah (God).
Responding to Mr Macron's campaign to defend such values - which began before the teacher was murdered - Mr Erdogan asked in a speech: "What's the problem of the individual called Macron with Islam and with the Muslims?".
In the wake of the remarks, a French presidential official told AFP news agency that France's ambassador to Turkey was being recalled for consultations, and would be meeting Mr Macron.
Seven people, including two students, have been charged over the beheading of French teacher Samuel Paty on 16 October near Paris.
The publication was targeted by extremists for publishing cartoons of the Prophet Muhammad.
Earlier this month, Mr Macron described Islam as a religion "in crisis," and announced plans for tougher laws to tackle what he called "Islamist separatism" in France.
Some in Western Europe's largest Muslim community have accused Mr Macron of trying to repress their religion and say his campaign risks legitimising Islamophobia.
France recalls Turkey envoy after Erdogan says Macron needs 'mental check'2
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