Eight other people were injured and 21 were rescued by Malta’s armed forces.
The armed forces deputy commander Colonel Edric Zahra told reporters that the incident happened at about midday (around 11:00 GMT) on Friday when the eight-metre (26-foot) migrant boat was 6.5km (four miles) south of Malta.
“The boat capsized suddenly while the rescue operation was under way,” he said.
“Eight are receiving medical care in hospital and unfortunately five were brought ashore dead,” he said, adding that the deceased included four men and one woman.
Among the injured were two people who swallowed a considerable amount of seawater and fuel.
Some 21 migrants were rescued and taken to a migrant centre. The passengers are believed to have set sail from Libya, but they hail from Egypt, Eritrea, Ghana and Syria.
Search operations were continuing offshore to ensure no other passengers remained in the sea.
The armed forces said they had been alerted earlier on 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 looked 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.”
He said there had been no collision, but the boat capsized “due to instability” as the passengers moved around.
The armed forces later sent more boats to try to help, and a police investigation was launched.
Malta rescued 380 migrants at sea in 2023 – its lowest annual total in years and just 10 percent of the number of irregular migrants who reached the island in 2019.
The country has also stepped up its relocation and repatriation efforts in recent years, relocating 159 irregular migrants and deporting roughly 1,700 others in 2023.
Most people who attempt the Central Mediterranean crossing from North Africa to Europe land in Italy, which recorded just under 160,000 arrivals last year.
Mediterranean sea crossings from North Africa to Italy or Malta are among the most dangerous migration routes in the world.
Last year almost 2,500 migrants died or went missing on those routes, the International Organization for Migration says.