The French president reportedly told Mr Rajoy France stands behind Madrid following riots in Catalonia after the Spanish government deemed the region’s independence referendum illegal.
The insider said: “The president underlined his support for Spain’s constitutional unity.”
But the source did not comment on whether Mr Macron had explicitly condemned the excessive use of force by Spanish police against people attempting to vote in Catalonia’s independence referendum over the weekend.
More than 800 people were injured on Sunday as riot police wielded batons and fired bullets at crowds attempting to cast their ballot in Catalonia’s banned referendum.
Mr Rajoy, who claims that the referendum is “illegal”, later hailed the police for carrying out their duties and upholding the law.
However, Mr Macron’s backing of the Spanish prime minister has been slammed by his left-wing and centrist opponents, who were quick to condemn the violent police tactics.
French far-left opposition party leader Jean-Luc Mélenchon said that Mr Rajoy had committed a “terrible mistake” by attempting to stop the referendum, and denounced the “inexcusable” use of violence by police.
Mr Mélenchon also urged Mr Macron’s government to “step in” and prevent the situation from descending further into chaos.
The Socialist party also said that it was dismayed by the violence, and urged Spain to “negotiate a deal” with Catalonia.
Leftist Benoît Hamon condemned the Spanish government’s “threatening” behaviour, while the centrist MoDem party echoed the Socialists by denouncing Mr Rajoy’s grave “mistake”.
Hundreds of thousands of people took to the streets of Barcelona, Catalonia’s regional capital, on Tuesday to protest against Spanish police brutality.