The Italian coastguard service confirmed the ship, also called the Louise Michel, had been seized.
It said the Louise Michel had been ordered to dock in the port of Trapani after conducting a rescue operation in Libyan waters "but had disobeyed that order and headed out to three other migrant boats."
The vessel - which was conducting life-saving operations to pick up people in distress in the Mediterranean Sea - was impounded in Lampedusa on Saturday.
The far-right government of Prime Minister Giorgia Meloni has vowed to curb the number of would-be asylum seekers landing in Italy.
It has passed a controversial law that forces charity ships to only perform one rescue mission at a time before returning to a port designated by the authorities, something critics say increases the risk of people drowning.
"We know of dozens of boats in distress right in front of the island (Lampedusa) at this very moment, yet we are being prevented from assisting. This is unacceptable!" the German charity said on Twitter on Sunday.
Meloni's government accuses charity rescue ships of encouraging migrants and of helping people-traffickers -- even though the life-saving vessels only pick up a small percentage of the people seeking to reach the EU via Italy's shores.
Critics of the new law on charity ships say it contradicts "international maritime, human rights and European law" and increases the risk of deaths at sea.
The charity vessels often perform multiple rescues to save people in distress in the Mediterranean before heading back to shore.
The International Maritime Organisation, a United Nations body, estimates 1,417 people disappeared in the Mediterranean Sea in 2022.
Many of those who attempt the crossing -- including families fleeing conflict, persecution or abject poverty -- do so on flimsy, overcrowded boats.