The Just Fitz III plucked 44 migrants from a rickety wooden boat late Monday after they ran into difficulty during the perilous crossing from North Africa.

The Marshall Islands-flagged vessel, which had been headed to Tunisia, was diverted to help the migrants as they floundered some 60 nautical miles south of the Italian island of Lampedusa, in Malta's search and rescue zone.

Valletta said those rescued at sea should be taken to the nearest safe port, on Lampedusa.

But Italy's new and hardline interior minister Matteo Salvini, the head of the far-right League, has vowed to stop migrant arrivals.

"Following the refusal of Italy to provide for the nearest place of safety, shelter and logistical support to the ship and in view of deteriorating weather conditions affecting the area," Malta agreed to take the migrants, the army said.

An offshore patrol vessel picked up the migrants from the Just Fitz III and was expected to disembark them on Malta late Wednesday.

- 'Dangerously toxic' -

It is not the first time rescued migrants in the Mediterranean have found themselves in limbo due to a row over who should take them in.

In June, Italy's new populist government turned away a rescue boat carrying 630 people, which was also rejected by Malta, forcing the vessel to remain at sea until Spain offered them safe haven.

Shortly afterwards, Italy and Malta refused a second vessel carrying nearly 250 migrants.

Later that month a Danish cargo ship owned by Maersk, the world's leading container shipping company, waited offshore for three days for instructions on what to do with the 108 migrants it had rescued, before Rome relented and allowed it to dock.

The UN Refugee Agency and the International Organization for Migration (IOM) warned Wednesday that the "political discourse concerning refugees and migrants, particularly those arriving by boat, has become dangerously toxic".

"Arrival numbers are falling but the rate at which people are losing their lives is on the rise," UN refugee chief Filippo Grandi said.

"We cannot forget that we are talking about human lives. Debate is welcome -- scapegoating refugees and migrants for political gain is not".

- 'White-gloved Nazis' -

Salvini supports a deal between Italy and Libya, forged under the previous, centre-left government, under which the Libyan coast guard intercepts migrants and returns them to the conflict-torn country.

Pope Francis compared those who send migrants back to hellish prisons in Libya to Nazis and Fascists.

"I am thinking of a film that witnesses to the situations of some prisons in North Africa built by human traffickers," he said in reference to Libya in an interview published Wednesday.

"When governments send back those who have survived, the traffickers put them in these prisons where the most horrible torture takes place.

"Today we beat our breasts for what the Communists, Nazis and Fascists did... but today? Does this not happen today? Certainly! And it is done with white silk gloves!" he said.