Sea-Watch 3 skipper Carola Rakete faced jail time on Saturday after forcing her way into Italy's Lampedusa port with rescued migrants to end a long standoff with authorities.
Sea-Watch spokesman Ruben Neugebauer said the German captain, 31, was seized after bringing the ship into port without authorisation late on Friday.
Ms Rakete, described as a "pain in the neck" by Italy's far-right Interior Minister Matteo Salvini, was detained for forcing her way past a police boat that tried to block her, a crime punishable by three to 10 years in jail.
She was escorted from her ship and taken away as Mr Salvini slammed what he termed a "criminal act, an act of war," demanding that she be imprisoned.
"Humanitarian reasons cannot justify unacceptable acts of violence towards those wearing uniform at sea," regional prosecutor Luigi Patronaggio said.
Ms Rakete will appear before a state prosecutor within 48 hours, her lawyer Leonardo Marino said.
🔵 Statement of our Captain, #CarolaRackete, before entering Port with the #SeaWatch3.
— Sea-Watch International (@seawatch_intl) June 29, 2019
“We are proud of our captain, she did exactly the right thing. She upheld the law of the sea and brought people to safety." – #SeaWatch chairman Johannes Bayer pic.twitter.com/lfZ16Pq9F1
She had apologised for putting the police speedboat and the safety of its occupants at risk.
The 40 migrants on board were allowed to disembark and were taken to a reception centre.
Some were smiling, while others were in tears as they prepared to travel to France, whose Interior Ministry said it would take in 10, or to Germany, Finland, Luxembourg or Portugal.
The Italian coastguard then seized the ship, anchoring it just off the coast.
"We put ourselves in the way to prevent the ship from entering the port," a police officer said in video posted on social media. "If we had stayed there it would have destroyed our speedboat.
Residents and activists gathered on the pier to watch the Sea-Watch 3 dock.
Supporters applauded Ms Rakete, while others shouted "handcuff her", "shame" and "get lost".
Former Italian ports minister Graziano Delrio said he was pleased that "the people's suffering is over".
German Foreign Minister Heiko Maas called for a "swift clarification" of the charges against Ms Rakete.
"Saving lives is a humanitarian duty," Mr Maas said. "Sea rescues must not be outlawed."
His position was echoed by Luxembourg Foreign Minister Jean Asselborn, while France's Christophe Castaner said that Italy's decision to close its ports to those rescued at sea was against maritime law.
The dreadlocked skipper has become a left-wing hero in Italy for challenging Mr Salvini's "closed-ports" policy and her charity's head, Johannes Bayer, said Sea-Watch was "proud of our captain".
"She did exactly the right thing. She upheld the law of the sea and brought people to safety," Mr Bayer tweeted.
But Mr Salvini, who leads the far-right League party, welcomed Ms Rakete's arrest.
"Mission accomplished," he tweeted. "Law-breaking captain arrested. Pirate ship seized, maximum fine for foreign NGO."
Mr Salvini's hardline immigration stance has boosted his popularity.
Italian Prime Minster Giuseppe Conte, in Japan for the G20 meeting, said: "I don't want to take the place of the judiciary but the laws exist, whether we like it or not."
Sicilian prosecutors have launched a probe into Ms Rakete on suspicion of aiding illegal immigration.
With Italy restricting port entry, Sea-Watch 3 was stuck in the Mediterranean during a heatwave after rescuing 53 migrants off the coast of Libya 17 days ago. Some had been allowed to disembark.
Almost 500 migrants have landed in Italy in the past 16 days, the Interior Ministry said.
Meanwhile, the founder of Spanish migrant rescue charity Proactiva Open Arms said he was prepared to risk prison to save lives in the Mediterranean.
"If I have to pay the price through prison time or a fine to save the lives of some people, then I will do so," Oscar Camps said.
The Open Arms ship took to the waters off the Libyan coast on Thursday, a decision that could result in a Spanish fine of up to €900,000 (Dh3.7 million), Mr Camps said.
