The accident occurred about two weeks after another boat carrying mainly Ethiopian migrants sank off the Djibouti coast, claiming several dozen lives, on the perilous so-called Eastern Migration Route from Africa to the Middle East.
"Tragedy as boat capsizes off Djibouti coast with 77 migrants on board including children," the International Organization for Migration, IOM said in a post on X, formerly Twitter.
"At least 28 missing. 16 dead," the migration agency said, adding that the IOM’s branch in Djibouti was "supporting local authorities with search and rescue effort."
Yvonne Ndege, a spokeswoman for the agency, said that the 16 fatalities included children and an infant, without offering further details.
Ethiopia's ambassador to Djibouti, Berhanu Tsegaye, said on X that the boat was carrying Ethiopian migrants from Yemen and that the accident occurred on Monday night off Godoria in northeastern Djibouti.
He said 33 people, including one woman, survived.
Another boat carrying more than 60 people sank off the coast of Godoria on April 8, according to the IOM and the Ethiopian embassy in Djibouti.
The IOM said at the time that the bodies of 38 migrants, including children, were recovered, while another six people were missing.
The Ethiopian embassy had said the boat was carrying Ethiopian migrants from Djibouti to war-torn Yemen.
Each year, many tens of thousands of African migrants brave the "Eastern Route" across the Red Sea and through Yemen to try to reach Saudi Arabia, escaping conflict or natural disaster, or seeking better economic opportunities.
"On their journeys, many face life-threatening dangers including starvation, health risks and exploitation — at the hands of human traffickers and other criminals," the IOM said in a statement in February.
Ndege said the IOM's data from 2023 showed that "the number of people trying to cross is on the rise."
According to the IOM, Ethiopians make up 79 percent of some 100,000 migrants who arrived in Yemen last year from Djibouti or Somalia, the remainder being Somalis.
Africa's second most populous country, Ethiopia is blighted by various conflicts and several regions have suffered from severe drought in recent years.
More than 15 percent of its 120 million inhabitants depend on food aid.
In February, the IOM said that according to its Missing Migrants Project at least 698 people, including women and children, had died crossing the Gulf of Aden from Djibouti to Yemen last year.