The boat was carrying documented Somali refugees who were travelling from Yemen to Sudan. At least 80 survivors were taken to hospital.
At least 42 Somali refugees were killed off the coast of Yemen late on Thursday when a helicopter attacked the boat they were travelling in, the International Organization for Migration said on Friday.
"Forty-two bodies recovered," Joel Millman, spokesman for the Geneva-based agency, told AFP in an email after earlier reports put the fatalities at more than 30.
Coast guard Mohamed al-Alay said the refugees were carrying official UNHCR documents. They were on their way from Yemen to Sudan when they were attacked by an Apache helicopter near the Bab el Mandeb strait.
A sailor who had been operating the boat, Ibrahim Ali Zeyad, said 80 refugees were rescued and hospitalised after the incident.
It was not immediately clear who carried out the attack.
Hodeidah on the Red Sea is controlled by Iran-allied Houthi fighters who in 2014 overran Yemen's capital Sanaa and forced the Saudi-backed government of President Abd-Rabbu Mansour Hadi to flee into exile.
A Saudi-led coalition was formed in 2015 to fight the Houthis and troops loyal to former President Ali Abdullah Saleh who have fired missiles into neighbouring Saudi Arabia.
The Bab el Mandeb is a strategic waterway at the foot of the Red Sea through which nearly 4 million barrels of oil are shipped daily to Europe, the United States and Asia.