Italy's far-right interior minister has condemned the seizure of the ship, saying migrants on board should not have set foot in Italy. However, the condition of the refugees had swayed the authorities' opinion.
Italian prosecutors on Sunday impounded rescue vessel Sea-Watch 3 for breaching immigration rules despite government attempts to block the ship from reaching an Italian port.
The remaining 47 migrants disembarked at Lampedusa on Sunday evening as part of the order to seize the ship.
"The Italian authorities finally allowed the disembarkation of our remaining guests," Sea-Watch said in a tweet. "The constitution still has more power than a Minister, who disrespects the law according to the UN. We are grateful to the Italian people who defend solidarity."
Last year, Amnesty International accused the Italian government of "repressive management of the migratory phenomenon."
Since 2015, nearly half a million irregular migrants have made the dangerous journey across the central Mediterranean and made landfall in Italy, according to the International Organization for Migration (IOM).