The National Council of Resistance in Iran (NCRI), which includes the former rebel People's Mujahedeen of Iran (MEK), claimed that 100,000 Iranians attended the annual rally at Le Bourget, near Paris, on Saturday.
"The holding of this rally by those whose hands are stained with the blood of the Iranian people... Is unacceptable," said the message handed to French ambassador Francois Senemaud by senior foreign ministry official Abolqassem Delfi, state media reported.
The US State Department listed it as a "terrorist organisation" in 1997.
After the US-led invasion of Iraq in 2003, its remaining fighters were disarmed and placed in camps where many of them remain with their families to this day.
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It was removed from terrorist watch lists by the European Union in 2008 and the United States in 2012.
Delfi said NCRI was linked to radical jihadist organisations such as "the Taliban, Al-Qaeda and the Islamic State" group.
He also dismissed as "inappropriate" comments made in France against Iran, without elaborating.
"The French government has no contact whatsoever with the People's Mujahedeen of Iran," said the spokesman, noting that the group held "violent and un-democratic" positions.
On Tuesday, Iranian government spokesman Mohammad Bagher Nobakht described the NCRI as an "annihilated terrorist group" and a "stinking corpse".
"The Islamic Republic of Iran will continue to confront this hypocritical little group and will condemn any government" that supports it, he told the official IRNA news agency.
And Foreign Minister Mohammad Javad Zarif has called the rally a "political game" where attendees "take part every year and support terrorists".