Rescue workers were searching the area for any other possible victims, the army's deputy commander Colonel Edric Zahra told a press conference.
"The boat capsized suddenly while the rescue operation was underway," he said.
The armed forces (AFM) had been alerted earlier Friday to a boat carrying several migrants close to fish farms off Zonqor on Malta's southern coast.
A surveillance plane confirmed the location and a patrol boat was dispatched to the area.
A photograph released by the armed forces showed the patrol boat nearing the migrant vessel, with some on board wearing what look like red life jackets.
"These migrant boats are usually heavily loaded with people. The chances are that when people move about, the boat loses balance," Zahra said, adding that "the migrants ended up in the water."
"Eight are receiving medical care in hospital and unfortunately five were brought ashore dead," he said, adding that the dead were four men and a woman.
The migrants are believed to have set sail from Libya but hail from Egypt, Eritrea, Ghana and Syria.
Around 380 migrants arrived on Malta by boat last year, according to the UN's refugee agency.
Most people who attempt the Central Mediterranean crossing from North Africa to Europe land on Italy, which last year recorded just under 160,000 arrivals.
The Central Mediterranean is the world's deadliest migration route, with 2,498 deaths recorded last year, a 75 percent increase on the previous year according to the International Organization for Migration.
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