"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.
Saudi Arabia, which has been leading a military aggression against Yemen to restore the impoverished country's former government to power, has been blamed for the killings late last week off the western port city of Hudaydah.
Somalia, which is a member of the coalition fighting the Houthi fighters, has also called for a probe into the raid.
The International Organization for Migration has said it believed the boat was headed for Sudan.
Saudi Arabia has been leading a deadly military campaign against Yemen since March 2015. The kingdom has also imposed an aerial and naval blockade on its southern neighbor.
According to the United Nations humanitarian coordinator for Yemen, Jamie McGoldrick, the Saudi military campaign has claimed the lives of 10,000 Yemenis and left 40,000 others wounded.
McGoldrick told reporters in Sana’a earlier this year that the figure was based on casualty counts given by health facilities and that the actual number might be higher.
However, local Yemeni sources have put the death toll from the Saudi war at over 12,000, including many women and children.
Despite a two-year war that has 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.