The Humanity 1 was ordered to vacate the port of Catania after disembarking 144 rescued migrants. They included women with children, more than 100 unaccompanied minors and people with medical emergencies.

The captain refused to comply “until all survivors rescued from distress at sea have been disembarked,” said SOS Humanity, the German charity that operates the ship. The vessel remained moored at the port as of mid-afternoon.

Humanitarian groups and two Italian lawmakers who traveled to Sicily protested the selection process as both illegal and inhumane. The procedure was part of directives ushered in by new Interior Minister Matteo Piantedosi as Italy again targets non-governmental organizations it has long accused of encouraging people trafficking in the central Mediterranean Sea.

“Free all the people, free them,” Italian lawmaker Aboubakar Soumahoro said in an emotional appeal directed at Premier Giorgia Meloni from the Humanity 1 rescue ship, calling her government’s new policy “inhuman.”

The passengers have faced ”trauma, they have faced everything that we can define as prolonged suffering, a hell,” Soumahoro said.

Italian authorities completed the process of identifying vulnerable migrants on the Humanity 1 overnight and asked the Geo Barents charity ship, which entered Italian waters with 572 rescued migrants, to proceed Sunday to Catania for the same vetting.

Two other boats run by non-governmental organizations remained at sea with no immediate change in status.

The charity ships have reported rescue people sleeping on floors and decks, the spread of fever-inducing infections and scabies, and food and medical supplies nearing depletion. Some migrants have been on the ships for more than two weeks.

The Humanity 1, carrying 179 rescued passengers, entered the Sicilian port at midnight Saturday. Two Italian doctors began identifying people needing urgent medical care after the ship’s doctor refused, said SOS Humanity spokesman Wasil Schauseil.

SOS Humanity considers all of the passengers vulnerable by definition after being rescued at sea, and deserving of a safe port under international law.

“Just like the already disembarked people, the survivors remaining on board the Humanity 1 are in an emergency condition,” the charity said. “They fled inhumane conditions from Libya and have since had to endure over two weeks at sea.”

Authorities allowed three women and a baby off the ship first, then one family followed by unaccompanied minors, who numbered over 100, Schauseil said.

“As we feared, not everyone was allowed to disembark,’’ Schauseil said.

“The doctors declared 36 people not in an emergency. After receiving the news, one person collapsed and lost consciousness and had to be taken by an ambulance,” Schauseil said.

“You can imagine the condition of the people. It is very devastating,” he said.

The Norway-flagged Geo Barents, carrying 572 migrants, arrived in Catania on Sunday afternoon. It entered Italian waters east of Sicily over the weekend to seek protection from storm-swollen seas.

“Once we get there, we will see what they mean by vulnerable people and if the other people can get off or not. Because if it is not like this, it would be an illegal action,’’ Riccardo Gatti, the search and rescue team leader on the Geo Barents, said.

Two other ships carrying rescued migrants remained at sea.

The German-run Rise Above, carrying 93, sought a more protected position east of Sicily due to the weather, but spokeswoman Hermine Poschmann said Sunday that the crew had not received any communication from Italian authorities.

Poschmann described cramped conditions on the relatively small 25-meter ship.

The Ocean Viking, operated by the European charity SOS Mediteranee, with 234 migrants on board, remained in international waters, south of the Strait of Messina, and did not receive instructions to proceed to a port, a spokesman said Sunday. Its first rescue was 16 days ago.

The confrontational stance taken by Meloni’s government is reminiscent of the standoffs orchestrated by Matteo Salvini, now Meloni’s infrastructure minister in charge of ports, during his brief 2018-2019 stint as interior minister.

Italy’s new government is insisting the countries whose flags the charity-run ships fly must take in the migrants.

In a Facebook video, Salvini repeated his allegations that the presence of the humanitarian boats encourages smugglers.

Nongovernmental organizations reject the government’s interpretation, saying they are obligated by the law of the sea to rescue people in distress and that coastal nations are obligated to provide a safe port as soon as feasible.

While the humanitarian-run boats are being denied a safe port, thousands of other migrants reached Italian shores over the last week, either on their own or after being rescued at sea by Italian authorities. They account for 85 percent of all arrivals, according to Italy.