A Maltese patrol boat rescued a group of 85 migrants late Friday night and was to bring them to Malta on Saturday morning, the Armed Forces said.
The migrants, believed to be from North and East Africa, were in a sinking wooden boat, the army said.
Malta has spearheaded EU efforts to share migrants rescued in the central Mediterranean among several member states after rescue ships were refused entry by Italy.
The latest case involved the NGO rescue ship Alan Kurdi which picked up 60 migrants and after being refused entry in Italy was allowed to disembark the migrants at Malta on April 13 so that they could be shared between Germany, France, Portugal and Luxembourg.
The European Union's commissioner responsible for migration, Dimitris Avramopoulos, visited Malta on Tuesday and praised the island for its response to irregular migration across the Mediterranean.
"Without a doubt, Malta is facing great migration challenges compared to the size of the population," Avramopoulos said.
"Overall, at the EU level we have returned to pre-crisis levels of irregular arrivals, but in Malta arrivals increased in 2018 due to search and rescue operations in the Mediterranean and the volatile and precarious situation in Libya."
Malta took in 108 migrants in March after its soldiers stormed a small tanker which authorities say had been hijacked by three teenagers, one from Cote d'Ivoire and two from Guinea, who tried to force the boat to take them to Malta and not back to Libya after it had rescued them and other migrants.
The three are now in a Maltese juvenile jail awaiting trial. They have pleaded not guilty.
Another group of 87 migrants were also rescued by a Maltese patrol boat and brought to Malta later that month.
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