Thirty institutions were found after some 130 migrants left Djibouti when two ships abducted in raw waters were reported by the US Migration Agency on Wednesday.
Sixteen survivors were recovered, and the small East African Coast Guard continued to search and save the operation after the Tuesday accident. Witnesses said that the big waves caused the top of the overloaded boats about half an hour after the departure.
The 18-year-old survivor told the migration agency that he had boarded one of the boats with another 130 people, including 16 women. There was no immediate information on the second boat.
Thousands of migrants from the shattering Horn of Africa region every year from Djibouti start crossing the Bab al-Mandab Strait in the Arabian Peninsula, hoping to find work in the rich Gulf countries.
Most migrants are Ethiopian, young and male, the migration agency says.
Crossing is dangerous because smugglers in some cases force migrants on board before reaching their destination. Other boats have been shot when they are approaching Yemen, where the struggle continues between the government-backed forces supported by the Saudi-led coalition and the Houthi rebels.
"This tragic event shows the risks that vulnerable migrants face when they seek innocent lives better," said Lalini Veerassamy, Head of Migration Agency Djibouti.
The 'Missing Migrants Project' agency says that since 1994 at least 199 people have drowned Djibouti off the coast of Obok.
According to the project, more than 700 other deaths have taken place along the coast from the Horn of Africa to Yemen.
The route also shows the flow of migrants from Yemen to the Horn of Africa as people flee from war.