"Many questions remain unanswered on the circumstances of this horrific event," the head of the UN refugee agency, Filippo Grandi, said in a statement.
"We call on all parties to the conflict to make proper inquiries to ensure accountability and to prevent this from happening again," he added.
The Saudi-led coalition battling rebels in Yemen has said it was not responsible for the killings late last week off the rebel-held port of Hodeida.
Somalia, which is a member of the coalition fighting Yemen's Shiite Huthi rebels, has also called for a probe into the raid.
The International Organization for Migration has said it believed the boat was headed for Sudan.
Despite a two-year war that has cost more than 7 000 lives and brought the country to the brink of famine, Yemen continues to attract people fleeing the horn of Africa.
The United Nations refugee agency, UNHCR, says Yemen is hosting more than 255 000 Somali refugees.