Italy’s far-right interior minister, Matteo Salvini, has said he will refuse to authorise an EU deal that would result in his country taking in some of the 49 people who spent more than two weeks stranded onboard two private rescue ships in the Mediterranean.

The Maltese prime minister, Joseph Muscat, announced on Wednesday that the people, who were rescued by the German NGOs ships Sea-Watch 3 and Sea-Eye off the coast of Libya in December, would disembark in the Maltese capital of Valletta before being sent to Italy, France, Germany, Portugal, Ireland, Romania, the Netherlands and Luxembourg.

The ships, operated by two German charities, had been stranded in Maltese waters after Italy, Malta and other EU states refused to offer them a safe port.

Maltese military vessels ferried the passengers to land on Wednesday as part of the deal brokered by the EU. Many of them waved and cheered at cameras recording their arrival.

“The crisis wasn’t created by us. We’re not making a war against the NGOs, we’re appealing to all to respect the rules,” Muscat said after announcing the operation was to begin.

Salvini, who travelled to Poland on Wednesday to meet leaders of the ruling Law and Justice party, suggested that the Italian prime minister, Giuseppe Conte, should not have negotiated the deal.

“I won’t authorise migrant arrivals,” he said during a press conference in Warsaw with Polish interior minister, Joachim Brudziński. He criticised the distribution plan, arguing that the EU was “succumbing to the blackmail of [people] smugglers and NGOs. This risks becoming a huge problem.”

Muscat said that the deal would also result in the eight countries taking in 249 other people brought to Malta by its military patrol boats in December.

The Sea-Watch 3, with 32 rescued people on board, had been waiting off the coast of Malta for 19 days. Photograph: Federico Scoppa/AFP/Getty Images

Thirty-two of the stranded people are onboard Sea-Watch 3, which has been at sea for 19 days, while an additional 17 were rescued on 29 December by Sea-Eye. Rescuers have spoken about the turmoil among the rescued people as the standoff continued, with some jumping into the sea in an attempt to reach Malta.

Malta allowed the two ships to shelter from bad weather near its coast and for them to be resupplied with fresh food and water, but until now had refused to let those onboard disembark, arguing that they had been rescued beyond the country’s search-and-rescue zone.

Between 2,000 and 3,000 people rescued in the Mediterranean have been denied entry into Italy in similar standoffs since Salvini, who leads the far-right League, started a clampdown on immigration within days of coming to power last June. Earlier this week he clashed with Conte and his coalition partner, Luigi Di Maio, leader of the Five Star Movement, who both said that women and their children should be taken off the boats and brought to Italy.