The drama unfolded as the migrants were travelling from Djibouti to Yemen.
At least 20 migrants are dead after smugglers threw 80 from a boat off the eastern coast of Africa, according to the International Organization for Migration (IOM).
The drama unfolded as the migrants were travelling from Djibouti to Yemen, said Mohammed Abdiker, IOM's East & Horn of Africa regional director.
The migrants were hoping to reach the Gulf countries to find work.
Yvonne Ndege, a regional spokesperson for the IOM, told Euronews that the boat left Oulebi, Djibouti, with 200 migrants on board, including minors, at around 2.00 am local time.
They had been sailing for thirty minutes when smugglers shouted there were too many people on the boat and started throwing people overboard, she added.
Five bodies have been recovered so far.
Survivors are receiving medical treatment at the IOM Migrant Response Centre in Obock, the international agency said.
"Wednesday’s tragedy is further proof that criminals continue to exploit people desperate to improve their lives for profit regardless of the consequences,” said IOM Djibouti Chief of Mission, Stephanie Daviot.
“Smugglers and human traffickers must be prosecuted for their crimes, and new migration pathways established to allow people to pursue work opportunities abroad in a safe, legal and dignified manner," Daviot added.
Authorities in Djibouti have opened an investigation into the case and the IOM is assisting the survivors to give their account of the events to police, Ndege told Euronews.
"On a daily basis thousands of young Africans, some minors, are trying to reach the Gulf countries via Yemen in search of jobs," the spokesperson said.
"Many die in this way, are stranded, or become trapped in Yemen," she continued.
According to the IOM, this is the third such tragedy in less than six months, with more than 70 migrants killed.