The prospect of a penalty comes after a protracted standoff between the Spanish NGO Proactiva Open Arms and Italy's far-right Interior Minister Matteo Salvini finally came to an end. The boat spent six days anchored off Lampedusa before a local prosecutor ordered that the migrants be allowed to land and the vessel temporarily seized amid a probe of Salvini for banning their entry to port.
Many had spent 19 days on board the ship after being picked up while in difficulty trying to make the perilous journey from Libya to Europe in small boats.
There were initially 147 mainly African migrants on the ship, but all minors and some suffering health problems had already disembarked. As they walked down the gangplank one by one to the island's shore overnight, some could be seen limping or in bandages.
One named Mohammed, 23, told AFP: "I nearly went mad," explaining that he and other migrants had been left "to cook like spaghetti on our boat" after it broke down in the Mediterranean.
The prosecutor who inspected the ship and decided the migrants should be allowed to disembark said they had been plunged into "a state of extreme emotions".
They were "veering between fear of death in the event of returning to the country (Libya) and hope of a new life, even if it meant throwing themselves into the sea and swimming to the island (Lampedusa)", the prosecutor said in a report quoted by Italian media.
Last charity vessel
Salvini had banned all NGO rescue boats from entering Italian ports. With the Open Arms impounded, the only remaining charity vessel currently operating in the Mediterranean, the Ocean Viking, was still seeking a safe port for its 356 rescued migrants. The ship operated by French charities SOS Mediterranee and Doctors Without Borders (MSF) has been holding its position for ten days between Malta and Lampedusa.
"As maritime law stipulates, we've been asking Italian and Maltese search and rescue coordination centres for a safe port since we made our first rescue on August 9th," said Frederic Penard, head of operations for SOS Mediterranee. "For the time being we've had no reply from Italy and a rather negative one from Malta."
The Open Arms on Wednesday sailed to Porto Empedocle in Sicily where the prosecutor ordered it temporarily seized as part of his investigation.
Spain's Deputy Prime Minister Carmen Calvo told Spanish radio: "The Open Arms doesn't have a permit to rescue."
The vessel had in April been authorized to leave Barcelona, where it was immobilized for three months, to transport humanitarian aid to Greece. It was banned from heading to the seas off Libya, often the launchpad for migrants attempting to reach Europe, but went anyway.
A document from the directorate-general for Spain's merchant navy sent to AFP by the Proactiva Open Arms charity said it risks a fine of up to 901,000 euros ($1 million) for violating this ban.
Six European Union countries -- France, Germany, Luxembourg, Portugal, Romania and Spain -- had offered to take them all in.
Calvo said the military ship sent to Lampedusa could take charge of those migrants allocated to Spain if this agreement is implemented.
France said on Wednesday it was sending a delegation from its refugee agency, Ofpra, to look at the situation of the some 40 migrants it has agreed to take. France also said it was ready to take in "a large number of migrants" from the Ocean Viking, while repeating it would not take in the vessel itself.
A spokesman for the French presidency said the Ocean Viking should be allowed to dock "at the nearest port."
Sicily prosecutor Luigi Patronaggio intervened as part of a probe into alleged kidnapping and refusing to obey orders targeting Salvini.
Salvini hit back on Facebook about the decision to let the migrants off the boat, saying: "If anybody thinks they can scare me with the umpteenth complaint and wants a trial, they're mistaken."
A Spanish naval patrol boat, the Audaz, set off from Rota in southwestern Spain on Tuesday on a three-day trip to Lampedusa to fetch the Open Arms migrants.
Spain had tried to break the standoff over the migrants at the weekend by offering up its southern port of Algeciras, which the NGO said could "not be achieved" due to the distance and tensions on board.
Madrid then suggested Mallorca in the Balearic Islands, nearer but still around 1,000 kilometres (600 miles) from Lampedusa. The charity described the offer as "totally incomprehensible" and continued to demand the ship be allowed to dock in Lampedusa.
By Taimaz Szirniks