Macron brought up "the number of victims from the demonstrations", and the two leaders also decided to postpone French Foreign Minister Jean-Yves Le Drian's visit to Teheran this week to a later date, the Elysee said.
Twenty-one people have died and hundreds have been arrested in nearly a week of protests in Iran.
Macron's office said the French leader underscored that "fundamental rights including freedom of expression and freedom to demonstrate must be respected."
"We criticise the fact that a terrorist group has a base in France and acts against the Iranian people... and we await action from the French government against this terrorist group," Rouhani told Macron, according to a report on Iranian state television.
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Macron's office did not offer any comment on this matter but said the two leaders had evoked the 2015 nuclear accord, saying that the French president wanted its "strict application under international supervision" while Rouhani sought "the backing of the international community to defend this accord and respect the commitments undertaken."
General Rassul Sanairad, a political deputy to the head of Iran's powerful Revolutionary Guards, said yesterday the Mujahedeen-e-Khalq had been instructed by the Saudi rulers and some European states to "create insecurity" in Iran, Tasnim news agency reported.