Macron on Friday met with four prominent Iranian dissidents, all of them women, as protests have rocked Iran for weeks following the death in September of Mahsa Amini.
The 22-year-old had been arrested by the morality police for an alleged breach of the country's strict dress rules for women.
The meeting was "a flagrant violation of France's international responsibilities in the fight against terrorism and violence", foreign ministry spokesman Nasser Kanani said.
"We consider that France favours these sinister phenomena," he added.
US-based activist Masih Alinejad, who for years has led a campaign encouraging Iranian women to remove their obligatory headscarves, and Ladan Boroumand, co-founder of Washington-based rights group Abdorrahman Boroumand Center, were among those at the meeting.
Alluding to Alinejad, Kanani said it was "surprising that the president of a country that stands for freedom would degrade himself by meeting" her, charging that she had "tried to spread hate and carry out violent and terrorist acts in Iran and against Iran's foreign diplomatic missions".
"Macron's declarations of support for this so-called revolution led by these people" were "regrettable and shameful", Kanani said.
Macron on Friday after meeting the women spoke of his "respect and admiration in the context of the revolution they are leading".