A rift has opened within Italy’s populist coalition government over the fate of 49 people who remain stranded at sea in the Mediterranean onboard two private rescue ships.

Thirty-two of them are onboard the German NGO rescue vessel Sea-Watch 3, which has been at sea for 17 days after Italy and Malta refused it permission to dock. An additional 17 people were rescued off the coast of Libya on 29 December by a second vessel, which is operated by another German humanitarian group, Sea-Eye.

Between 2,000 and 3,000 people rescued in the Mediterranean have been denied entry into Italy in similar standoffs since Matteo Salvini, the deputy prime minister and leader of the far-right League, started a clampdown on immigration within days of coming to power last June.

As the Italian prime minister, Giuseppe Conte, tries to reach an agreement with other EU states to take in some of the stranded, Salvini has refused to relent, writing on Facebook that Italy’s ports “will remain closed to those who don’t respect the rules”. Salvini ignored a plea from Pope Francis on Sunday for European leaders to “show solidarity” and offer a safe port to the 49 people onboard the Sea-Watch 3 and the Sea-Eye.

Salvini also appears to be at odds with his coalition partner Luigi Di Maio, deputy prime minister and leader of the Five Star Movement (M5S). On Saturday Di Maio insisted Malta take responsibility for those onboard but that Italy would welcome the 10 women and their children who were among them.

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 refused to let those onboard disembark, arguing that they were rescued beyond the country’s search-and-rescue zone.

In response to Di Maio, Salvini, who is also interior minister, struck a dismissive tone, saying: “Migrants? I’m the one who decides.”

Di Maio said on Monday he supported his government’s tough immigration line but that he believed that the women and children ought to be taken in.

But clashes with the League has caused ruptures within Di Maio’s own ranks. The M5S expelled two senators, including Gregorio De Falco, for voting against a security bill drafted by Salvini that targets asylum rights. Two MEPs were also expelled for failing to follow party rules.

“I voted against the security bill because it is abnormal, unconstitutional and will produce a greater number of illegal [immigrants] and insecurity,” De Falco told the Guardian. “There are others in opposition - the far-right policies of the League are not the policies of the M5S.”

Dozens of mayors across Italy have also refused to implement the security bill.

De Falco said the closure of sea ports was not an official government measure and that Di Maio and Salvini were simply giving the impression of a united front.

“There are splits on many aspects. The two sides are not united nor, to tell the truth, is that the intention,” he said.

Rino Marinello, an M5S senatorr, said that while Italy should take in women and children from the two ships, other EU states needed to play their part.

“These migrants need medical assistance as soon as possible … but it is time that Europe makes new agreements for the resettlement of migrants,” he said.

“It also time for Europe to invest in Africa and improve peoples’ conditions there. We can’t just stare at Africa while human traffickers are making millions out of migrants.”

As the sparring continues, Frank Dörner, a doctor on the Sea-watch 3, said the rescued people were in a “dire situation”. A few days ago, one jumped into the sea in an attempt to reach Malta and was quickly brought back onboard.

“The situation is getting more and more unstable,” he said. “People were already traumatised when they reached our boat but every day the stress level is increasing.”