In Paris,demonstrators at the Place de la Republique carried signs reading "Saving lives: A duty not a crime," ''Save the Aquarius," and other slogans backing the ship.
Placard-waving supporters of the Aquarius also gathered in the southern port city of Marseille and in the northern city of Lille.
The Aquarius' operator, SOS Mediterranee, is urging European governments to find a new flag for the ship after Panama's maritime authority removed its registration. The aid group says without a flag, the ship will have to stay in port.
Migrant sea arrivals to Europe are sharply down this year but the issue of immigration is still a hot political topic across the continent.
The International Organization for Migration says that 1,741 migrants have drowned at sea this year trying to cross the Mediterranean.