Up to 50 young migrants were "deliberately drowned" by a people smuggler who chose to sacrifice their lives rather than risk arrest, the UN's migration agency said.
Survivors from the boat journey reported they were forced into the sea off the coast of Yemen after the trafficker in charge of their journey thought he spotted authorities.
The bodies of at least 29 victims were washed up on shore, where they were discovered by staff members at the International Organization for Migration (IOM).
At least another 22 people of around 120 people on the boat are still missing, the IOM said.
It said the passengers were mostly young people from Somalia and Ethiopia, who had paid people smugglers in the hope of finding a better life.
The average age of passengers on the boat was 16, it added.
The narrow waters between the Horn of Africa and Yemen have become a popular migration route for those hoping to reach the oil-rich Gulf countries.
The IOM says about 55,000 migrants have left Horn of Africa nations for Yemen since January, with most from Somalia and Ethiopia. A third of them are estimated to be women.
Migrants are braving the journey despite the war in Yemen as the violent conflict means there is no central authority to stop them travelling onward.
However the journey is fraught with danger, from the overloaded boats to the risk of being caught up in attacks in Yemen and the threat of falling victim to armed trafficking rings.
Many are fleeing desperate situations in their home states.
Some Somalis are desperate to avoid years of chaos at home with attacks by homegrown extremist group al-Shabab and deadly drought.
Meanwhile some Ethiopians have left home after months of deadly anti-government protests and a 10-month state of emergency.
More than 111,500 migrants landed on Yemen's shores last year, up from around 100,000 the year before, according to the Regional Mixed Migration Secretariat, a grouping of international agencies.