Sixteen survivors were recovered, and the tiny East African nation’s coast guard continued a search and rescue operation after Tuesday’s accident, the U.N. said in a statement.
Witnesses said large waves caused the overloaded boats to tip over about a half-hour after departing.
An 18-year-old survivor told the migration agency he had boarded one of the boats with another 130 people, including 16 women. There were no immediate details on the second boat.
Thousands of migrants from the turbulent Horn of Africa region set off every year from Djibouti to cross the Bab al-Mandab Strait for the Arabian Peninsula with hopes of finding work in rich Gulf countries.
The vast majority of the migrants are Ethiopian, young and male, the migration agency says.
The crossing is dangerous, with smugglers in some cases forcing migrants overboard before reaching their destination.
Other boats have been fired on as they approach Yemen, where fighting continues between pro-government forces backed by a Saudi-led coalition and Houthi rebels.
“This tragic event demonstrates the risks that vulnerable migrants face as they innocently search for better lives,” said the migration agency’s Djibouti chief of mission, Lalini Veerassamy.
The agency’s Missing Migrants Project says at least 199 people have now drowned off the Djibouti coast near Obock, where the latest capsizing occurred, since 2014.
More than 700 other deaths have occurred further off shore on the route from the Horn of Africa to Yemen, according to the project’s data.
The route also sees a flow of migrants from Yemen toward the Horn of Africa as people flee war.