An extraordinary standoff between the two vessels off the coast of the Mediterranean's Lampedusa island was broken when Captain Carola Rackete, 31, plowed into the smaller motorboat which was blocking her ship from port.
He said they violated the law by ignoring direct orders not to enter Italian waters as well as a special government measure that specifically banned the Sea-Watch 3 from Italian jurisdiction.
Italian Deputy Premier and Interior Minister, Matteo Salvini, attends a RAI state TV program in Rome, Wednesday, June 26, 2019.
Sea-Watch spokeswoman Giorgia Linardi said in a video posted on Twitter the ship attempted to enter port but was blocked by police and now stands a mile off Lampedusa port. "#CarolaRackete and her crew, to bringing the 40 people to safety", the charity said on Twitter.
The captain of an NGO rescue ship carrying 42 people has been arrested for breaking a naval blockade by an Italian military vessel that was trying to stop the vessel from disembarking in the Sicilian port of Lampedusa.
Rackete had already said that "for me, Lampedusa is the only option", discarding a priori any other port to disembark her passengers, including Spanish ports that would have shortened her 1400-km journey considerably and an offer from nearby Tunisia to receive the migrants there.
Salvini has called for her to be slapped with a hefty fine and face legal action, and he wants the ship seized.
Sea-Watch 3 was one of the first migrant rescue vessels to test new Italy's newest hardline migration laws.
Forty migrants have disembarked on a tiny Italian island after the captain of the German aid ship which rescued them docked without permission.
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"Humanitarian reasons can not justify unacceptable acts of violence towards those wearing uniform at sea", Italian media quoted regional prosecutor Luigi Patronaggio as saying.
But a Sicily-based prosecutor, Luigi Patronaggio, indicated otherwise.
With Italy restricting port entry, the vessel had been stuck in the Mediterranean during a heatwave since rescuing 53 migrants drifting in an inflatable raft off the coast of Libya on June 12.
The ship docked despite a coastguard boat trying to prevent her from doing so by sailing back and forth between the vessel and the pier, according to the Repubblica daily.
But even as the migrants' numbers dwindled as Italy cracked down on private rescue ships, many Italians lost patience, including economic migrants ineligible for asylum.
A judge will decide in a few days whether Rackete can be kept under arrest while the investigation continues.
The NGO's head, Johannes Bayer, said Sea-Watch was "proud of our captain".
Castaner used his statement to criticise unilateral moves by Italy and defend French and European Union support for Italy in handling migrant arrivals.
Democratic Party lawmaker Graziano Delrio, after disembarking himself, likened her actions to that of a driver of a Red Cross ambulance "which goes through a red light" to speed ailing patients to a hospital. The Italian government said it will not permit the ship's remaining 40 migrants to disembark after allowing 13 people off the vessel for medical treatment.