"Muslims are the primary victims of the 'cult of hatred,'" the minister, Mohammad Javad Zarif, tweeted, without directly addressing Macron.
"Insulting 1.9B Muslims—& their sanctities—for the abhorrent crimes of such extremists is an opportunistic abuse of freedom of speech. It only fuels extremism," he added.
Macron, who led a tribute to a history teacher beheaded this month by a Chechen teenager for showing caricatures of the Prophet Mohammad in class, declared war on "Islamist separatism", which he believes is taking over some Muslim communities in France.
Unlike some Muslim countries, Iran's clerical rulers have not called for a boycott of French goods. But several Iranian officials and politicians, including the heads of parliament and the judiciary, have condemned Macron for "Islamophobia", according to Iranian state media.
Ali Shamkhani, a close ally of Iran's top authority Supreme Leader Ayatollah Ali Khamenei said Macron's "irrational behaviour" displayed his "crudeness in politics".
"Otherwise he would not have dared to embrace Islam in his quest for leadership in #Europe," tweeted Shamkhani, secretary of Iran's Supreme National security Council.
"I suggest that he read more history and not rejoice in the support of a declining America & #Zionism."