Proactiva Open Arms, which helped the “Nuestra Madre Loreto” Spanish fishing vessel rescue the migrants, said Valletta had agreed to take them in amid worsening sea conditions.
“#NuestraMadreLoreto has completed the transfer to Maltese coastguard and the 11 rescued people will disembark shortly in safe harbour #Malta,” it said on Twitter.
Twelve migrants from Niger, Somalia, Sudan, Senegal and Egypt were rescued off the coast of Libya on November 22nd. One was later evacuated by helicopter after falling seriously ill from dehydration.
The migrants had originally set out from Libya and were found drifting in a rubber dinghy in Maltese waters. Spain had tried to get Tripoli to take them back, and was in talks with Italy and Malta too.
But Pascual Dura, captain of the aid vessel sheltering them, told AFP on Tuesday that both Rome and Valletta had refused to let them dock.
“I cannot sail north and south, east and west, fleeing bad weather, without having an answer. I cannot believe it's not possible to find these people shelter,” he said in a radio message on Saturday, according to Proactiva Open Arms.
The UN's human rights body repeated in September its view that Libya was “not meeting the criteria for being designated as a place of safety for the purpose of disembarkation following rescue at sea”.
The UNHCR pointed to the volatile security situation in the crisis-hit North African country as well as the particular risks for asylum-seekers, refugees and migrants who are often held in substandard detention conditions.
Abuse of migrants is widespread following the chaos which has reigned since the 2011 ousting of dictator Muammar Gaddafi.
Many of those intercepted or rescued at sea find themselves held in prison-like centres, or are sold by traffickers.
Shortly after Spain's Socialist Prime Minister Pedro Sanchez came to power in June, Spain welcomed the Aquarius charity-run rescue ship and its 630 migrants after Italy and Malta refused to harbour the vessel.
Spain also welcomed the Open Arms ship three times, but in September Madrid declined to receive the Aquarius again. Instead it negotiated the distribution of the migrants aboard the ship among several other European Union nations.