ROME — On Monday, it was Malta’s turn to get tough on immigration in Europe.

Prosecutors brought legal charges against a nongovernmental organization active in the rescue of migrants in the Mediterranean, arguing in a hearing that the captain of the Dutch vessel Lifeline had entered the country’s waters illegally and lacked a proper boat registration.

The ship docked in Malta last Wednesday after a weeklong dispute over who should take in the 234 migrants it was carrying after rescuing them from two rubber dinghies. The island agreed to allow it on the condition that the migrants, who had set off from Libya, would be distributed among European member states.

But on Monday, the Maltese authorities confiscated the rescue boat and began a case against its captain, Claus-Peter Reisch, 57, of Germany. Human rights advocates and other defenders of Mr. Reisch said they thought he was being used as a scapegoat.

“There was no mention in court of the captain violating international rules or about what happened during the rescue operation,” said Neil Falzon, the director of the Aditus Foundation, a Maltese human rights group that is offering legal assistance to Mr. Reisch. “They are targeting NGOs to target anyone dealing with immigrants.”