"The knife-wielding crew of the smuggling boat told passengers they would travel to the Somali city of Bossaso in a smaller boat to recharge a battery and then return as soon as possible. They never returned," the UNHCR statement said.
Three of the remaining passengers then swam ashore as the ship drifted closer to the Yemeni coast, but only two had survived before reaching the port city of Shihra.
Rescuers towed the stricken boat to shore, where the passengers were met by UNHCR staff and other humanitarian agencies.
The refugees, who paid up to $100 each for the journey, had been drifting near the Yemeni border in the Gulf of Aden without food or water for 18 days.
The UNHCR quoted survivors who said that most of the dead bodies were thrown overboard.
Journey from Africa
The UN agency said that more than 31,000 African migrants have arrived in Yemen this year, but another 500 have died or gone missing trying to make the journey from Africa.
Ron Redmond, a UNHCR spokesman based in Geneva, said: "UNHCR and its humanitarian partners are trying to do everything they can to prevent further tragedies, but the real solution to this ongoing crisis has got to be political, not humanitarian".
Between May and September, smuggling usually subsides because of stormy weather in the Gulf of Aden.
"With the early onset of calmer weather in August, smuggling resumed when 65 boats brought more than 2,500 desperate people to Yemen – nearly quadruple the number of arrivals for same month last year when 633 people landed in 10 boats," the statement said.
The UNHCR says a number of factors are responsible for refugee migrating from Somalia and Ethiopia, including displacement and the opening of new smuggling routes across the Gulf of Aden.