A helicopter opened fire on the vessel carrying over 140 passengers, killing 42 civilians and wounding 34, in an attack the report said was a violation of international humanitarian law.
"This civilian vessel was almost certainly attacked using a 7.62mm caliber weapon from an armed utility helicopter," said the report by the UN panel of experts presented to the council this week.
"The Saudi Arabia-led coalition forces are the only parties to the conflict that have the capability to operate armed utility helicopters in the area."
The helicopter was most likely operating from a naval vessel deployed by the coalition backing Yemen's government.
The coalition has denied that its forces were operating in the area of Hodeida when the vessel carrying Somali refugees in the Red Sea came under attack.
Major General Ahmed Assiri, spokesman for the coalition, dismissed the accusation and then told AFP "there has been no firing by the coalition in this zone."
Despite requests from the UN panel, the coalition, Egypt, the United Arab Emirates and the 31-nation Combined Maritime Forces have not shared information on the incident, the report said.
"The panel finds that the attack on this civilian vessel resulted in IHL violations ... and thus constitute a threat to peace, security and stability of Yemen," the report said.
Two other attacks by helicopters or naval vessels on March 15 and 16 on fishing vessels left 11 dead and 8 injured, it added.
Saudi Arabia leads an Arab military coalition backing the Yemeni government in a violent war against Yemen's Iran-allied Huthi rebels since March 2015.
The conflict has brought Yemen to its knees, with more than 60 percent of the population on the brink of famine and facing the world's worst cholera outbreak.
UN aid chief Stephen O'Brien this month blamed Yemen's warring sides and their foreign backers for a cholera outbreak that he described as "man-made" and a "direct result of the conflict."
There are now more than 400,000 suspected cases of cholera in Yemen and nearly 1,900 people have died.