Maltese coastguards rescued 100 migrants and recovered two bodies from a small boat south of the island on Wednesday.
The boat the migrants were on was taking in water and two had already died by the time rescuers reached them, the Armed Forces of Malta (AFM) said in a statement.
After the AFM vessel carrying the rescued migrants arrived in Malta's Grand Harbour, the migrants were transferred to a detention centre.
Meanwhile, in a statement the Maltese government stressed that it always adhered to international laws and applicable conventions when it comes to rescuing migrants at sea.
The government was responding to Italian Interior Minister Matteo Salvini, who has accused Malta of not fulfilling its commitment to take in 50 out of some 450 migrants who were allowed to land in Italy five weeks ago.
"The Maltese authorities have already been in contact with the Italian authorities to fulfil their pledged commitments as soon as possible. Nevertheless, the Italian authorities have not provided any tangible procedure for Malta to follow," the statement said.
"On the other hand, the government noted that Italy has unfortunately not yet fulfilled its commitments on the redistribution mechanism which was initiated by Malta with respect to the immigrants disembarked in Malta on board of the MV Lifeline on 27 June," it said.
The Lifeline vessel, run by a German NGO of the same name, was allowed to dock in the Maltese capital Valletta with more than 200 migrants on board after several European countries, including Italy, agreed to take some of them in.
Malta insisted it "always participated in solidarity mechanisms and was the first European Union member state to fulfil its commitments with regard to the European Commission's solidarity mechanism with respect to Italy and Greece".