The French foreign ministry said the "baseless" calls for a boycott were being "pushed by a radical minority".
French products have been removed from some shops in Kuwait, Jordan and Qatar.
Meanwhile, protests have been seen in Libya, Syria and the Gaza Strip.
The backlash stems from comments made by Mr Macron after the gruesome murder of a French teacher who showed cartoons of the Prophet Muhammad in class.
The president said the teacher, Samuel Paty, "was killed because Islamists want our future", but France would "not give up our cartoons".
Depictions of the Prophet Muhammad can cause serious offence to Muslims because Islamic tradition explicitly forbids images of Muhammad and Allah (God).
On Sunday, Mr Macron doubled down on his defence of French values in a tweet that read: "We will not give in, ever."
Political leaders in Turkey and Pakistan have rounded on Mr Macron, accusing him of not respecting "freedom of belief" and marginalising the millions of Muslims in France.
On Sunday, Turkish President Recep Tayyip Erdogan suggested, for a second time, that Mr Macron should seek "mental checks" for his views on Islam.
Similar comments prompted France to recall its ambassador to Turkey for consultations on Saturday.
How widespread is the boycott on French products?
Some supermarket shelves had been stripped of French products in Jordan, Qatar and Kuwait by Sunday. French-made hair and beauty items, for example, were not on display.
In Kuwait, a major retail union has ordered a boycott of French goods.
The non-governmental Union of Consumer Co-operative Societies said it had issued the directive in response to "repeated insults" against the Prophet Muhammad.
In a statement, the French foreign ministry acknowledged the moves, writing: "These calls for boycott are baseless and should stop immediately, as well as all attacks against our country, which are being pushed by a radical minority."
Online, calls for similar boycotts in other Arab countries, such as Saudi Arabia, have been circulating.
A hashtag calling for the boycott of French supermarket chain Carrefour was the second-most trending topic in Saudi Arabia, the Arab world's largest economy.
Meanwhile, small anti-French protests were held in Libya, Gaza and northern Syria, where Turkish-backed militias exert control.
Why is France embroiled in this row?
Mr Macron's robust defence of French secularism and criticism of radical Islam in the wake of Mr Paty's killing has angered some in the Muslim world.
Turkey's Mr Erdogan asked in a speech: "What's the problem of the individual called Macron with Islam and with the Muslims?"
Meanwhile Pakistani leader Imran Khan accused the French leader of "attacking Islam, clearly without having any understanding of it".
"President Macron has attacked and hurt the sentiments of millions of Muslims in Europe & across the world," he tweeted.
Earlier this month, before the teacher's killing, Mr Macron had already announced plans for tougher laws to tackle what he called "Islamist separatism" in France.
He said a minority of France's estimated six million Muslims were in danger of forming a "counter-society", describing Islam as a religion "in crisis".
Cartoons caricaturing the Islamic prophet have a dark and intensely political legacy in France.
In 2015, 12 people were killed in an attack on the offices of French satirical magazine Charlie Hebdo, which had published the cartoons.
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.
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‘Boycott French products’ launched over Macron’s Islam comments