The attack, which Yemen's Shiite rebels blamed on a Saudi-led coalition, highlighted the perils of a heavily used migration route running from the Horn of Africa to the oil-rich Gulf, right through Yemen's civil war.
The coalition has been heavily bombarding the nearby coast around the Yemeni port of Hodeida, where it accuses the rebels, known as Houthis, of smuggling weapons in small boats. There was no immediate coalition comment.
Al-Hassan Ghaleb Mohammed told The Associated Press the boat left from Ras Arra, along the southern coastline in Yemen's Hodeida province, and was 30 miles (50 kilometers) off the coast, near the Bab al-Mandab strait, when the military vessel open fire, followed by the helicopter gunship.
He described a scene of panic in which the terrified refugees waved flashlights, apparently to show they were not combatants. He said the helicopter then stopped firing, but only after dozens had been killed. Mohammed was unharmed in the attack.
The UN refugee agency said on its Twitter account that it was "appalled by this tragic incident, the latest in which civilians continue to disproportionately bear the brunt of conflict in Yemen."
A top official with the UN's migration agency said 42 bodies were recovered from the attack, which took place around 3 AM today. Mohammed Abdiker, emergencies director at the International Organization for Migration in Geneva, called the assault "totally unacceptable" and said those responsible should have checked who was aboard the boat before firing on it. He said about 75 men and 15 women who survived the attack were taken to detention centers, and some bodies were laid in a fish market in Hodeida because of a lack of space in mortuaries.
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