"Police are at the scene carrying out arrests. SOS Mediterranee staffers are safe and sound but in a state of shock," the aid agency tweeted.
The charity said the activists belonged to the Identitarian movement (Les Identitaires), which opposes France’s so-called Islamization and uncontrolled immigration.
The agency has been at the heart of a dispute over the Aquarius, a ship it hired together with Doctors Without Borders to rescue African migrants stranded at sea while trying to reach Europe.
In June, the vessel, which had over 600 migrants on board at the time, was denied entry by Italian and Maltese ports. Spain eventually allowed the Aquarius to dock and the migrants were accommodated by several EU countries.