The German captain of a ship that rescued 53 migrants off the coast of Libya was arrested and accused of trying to sink a police boat after reaching landfall in Italy.

The vessel, named Sea-Watch 3, had reached the Italian port of Lampedusa on Saturday after a two-week standoff with police.

Captain of the migrant ship, Carola Rackete, 31, was arrested upon arrival and subsequently accused by Matteo Salvini, Italy's Deputy Prime Minister, of trying to sink a police boat during the ordeal, according to the BBC.

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Carola Rackete, the 31-year-old Sea-Watch 3 captain,was escorted off the ship by police and taken away for questioning.

Carola Rackete, the 31-year-old Sea-Watch 3 captain,was escorted off the ship by police and taken away for questioning. (REUTERS)

"She tried to sink a police launch with officers on board at night," Salvini said. "They say 'we're saving lives', but they risked killing these human beings who were doing their job, it's clear from the videos."

Salvini added that Rackete's actions could be classified as an act of war.

Sea-Watch 3 captain Carola Rackete is seen on board the vessel at sea in the Mediterranean, just off the coasts of the southern Italian island of Lampedusa, on Thursday.

Sea-Watch 3 captain Carola Rackete is seen on board the vessel at sea in the Mediterranean, just off the coasts of the southern Italian island of Lampedusa, on Thursday. ((ANSA/Matteo Guidelli via AP))

"A vessel weighing hundreds of tonnes tried to ram... a police launch with officers aboard, who managed to get out of the way to save their lives. That's a criminal act, an act of war."

E.U. countries have agreed to take on 40 of the migrants, while the BBC reported that 13 have been taken into custody for health reasons.

Rackete was recorded walking off the ship into the hands of Italian police custody, who led her away without handcuffs and into a police vehicle.

She could face 10 years in prison if convicted of attacking a police boat.

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The Vessel carrying the migrants was operated by German charity, Sea-Watch, which conducts civil search and rescue operations in the Mediterranean. The non-profit says Sea-Watch 3 was forced to enter Italian waters because they were out of options in making sure the migrants reached land safely.

An Italian Coast Guard boat patrols next to the Sea-Watch 3 vessel, in the Mediterranean Sea just off the coasts of the southern Italian island of Lampedusa on Thursday.

An Italian Coast Guard boat patrols next to the Sea-Watch 3 vessel, in the Mediterranean Sea just off the coasts of the southern Italian island of Lampedusa on Thursday. ((ANSA/Matteo Guidelli via AP))

Before joining Sea Watch, Rackete had previously taken part in missions for the environmental group Greenpeace as well as other research organizations.

After the incident, some on Twitter spoke out on behalf of the Captain, with some calling her a hero.

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The Sea Watch chairman Johannes Bayer expressed support for Rackete and tweeted that he was "proud of our captain".