Another 30 are reported missing by survivors who were rescued by a Spanish trawler more than a week after their boat lost power.
The BBC's Hasna Maki in Djibouti says the survivors are very weak and undernourished.
Most are believed to have spent 10 days without water.
Fleeing anarchy
More than 90 survivors have been taken to a medical centre staffed by the French military, who have a base there.
Three of the dozen who were taken to hospital have since died.
The group, made up largely of Ethiopians who lived in Somalia, had left from the town of Bossasso, in the autonomous Somali region of Puntland.
On Wednesday morning, the Ethiopian and French ambassadors in Djibouti visited the survivors at the centre where they are recovering from their ordeal.
In April, more than 90 people were reported to have drowned when their boat sank on its way from Somalia to Yemen.
Last year, a boat captain was arrested for allegedly ordering at least 86 Somalis to jump into the sea after his ship developed engine trouble.
Somalia has been without an effective central government since 1991, when Siad Barre was overthrown.
A peace conference between rival warlords currently being held in neighbouring Kenya has failed to end 11 years of anarchy and fighting.