An Italian charity ship has rescued about 50 people from a rubber boat off the coast of Libya, prompting Rome to warn it is ready to stop private vessels “once and for all” from bringing rescued migrants to Italy.

The interior minister, Matteo Salvini, has repeatedly declared Italian waters closed to NGO rescue vessels and has left several of them stranded at sea in the past in an attempt to force the rest of Europe to take in more asylum seekers.

The Mediterranean collective of aid groups and associations that runs the ship tweeted: “Mare Jonio has just rescued a rubber boat in distress that was sinking with around 50 people on board.”

Volunteers onboard the Mare Jonio pulled the migrants – reportedly including 12 children – from the dinghy 40 nautical miles off the coast of Libya. The ship was heading to the Sicilian island of Lampedusa, “the closest safe haven in the area where the rescue was performed”, Mare Jonio’s press office in Rome said in a statement on Tuesday morning.

A Libyan coastguard vessel had approached the dinghy while the rescue was under way, but left the group to the Mare Jonio, which was expected to request permission to bring them to Italy.

After the release on Tuesday morning of an eight-page directive on the laws regarding rescue operations, which said “there must be sanctions for those who explicitly violate international, European and national rescue regulations”, Salvini tweeted: “The ports have been, and remain, closed.”

He described the passage of rescue ships in territorial waters as “detrimental to the order and security of the Italian state”.

After the directive was issued, Mare Jonio was approached by two Italian police boats. They ordered the captain to stop the engine 1 mile from Lampedusa and dozens of officers then boarded the vessel to carry out inspections.

Meanwhile, at least a dozen of people are missing off the coast of Sabratha, in Libya, after a boat capsized, according to the International Organisation for Migration. Fifteen survivors were rescued and returned to Libya where they were treated by medical staff. OIM says those injured are critical.

In August, prosecutors in Agrigento, Sicily, placed Salvini under investigation for the alleged kidnapping and detention of 177 people whom he prevented from disembarking from the Italian coastguard ship Ubaldo Diciotti.

The vessel had been docked for six days at the Sicilian port of Catania as Salvini maintained a standoff with the EU in an attempt to push other member states to take in the migrants.

In January, a court in Italy ruled he should be tried for kidnapping and, at the end of March, the accusations against him will be put to senators, who will vote either for him to stand trial or for the proceedings to be halted.

“If what I did means I’m a kidnapper,” Salvini said, “well, then you can consider me as a kidnapper for the coming months.”

The Italian flag on the 38-metre Mare Jonio will make it harder for Salvini to prevent it from docking, though he could still try to stop people disembarking. The ship has been bought and equipped by a coalition of leftwing politicians, anti-racist associations, intellectuals and figures in the arts, under the supervision and support of two NGOs – Proactiva of Spain and the aid group Sea Watch. Its mission has been called Mediterranea.

Should the Mare Jonio be refused permission to dock, it would be the first such standoff between the government and an Italian-flagged ship.

Opposition parties have asked the prime minister, Giuseppe Conte, to intervene and allow the passengers to disembark.

Mare Jonio’s press office said: “We rescued these migrants twice – from shipwreck and from the risk to be captured and taken back to suffer again the tortures and horrors from which they were fleeing.

“This is something that happens every day in silence. Because of our amazing crews at sea and on land, as well as because of the tens of thousands people that supported us in Italy, the Mediterranean today is not any more just a graveyard and desert.”

With EU support, Italy has been training the Libyan coastguard to intercept boats since 2017 as part of a controversial deal that has led to a sharp fall in numbers arriving in Italy.

NGO ships have drawn fire from Rome by attempting on occasion to stop migrants being taken back to crisis-hit Libya, which human rights organisations insist cannot be considered safe for repatriations.

The Mare Jonio is the only privately run rescue ship operating in the central Mediterranean. Others are either undergoing repairs, docked for a crew change or blocked by administrative or judicial hurdles.

This year, 348 people have been brought to safety in Italy, compared with 6,161 in the same period last year.

So far in 2019, 234 people have died in the Mediterranean, according to the International Organization for Migration.