The confirmation came after 72 passengers were reportedly missing in the accident in the day.
"Now our team of rescuers has found 39 corpses and search continues to recover all the corpses," Emanuelle Mulinbwa, a communication counselor of South Kivu province, told Xinhua.
More than 100 people were on board the vessel when it capsized on its course from Minova to Bukavu in the east of the Central African country.
Bad weather and high winds were linked to the accident, in which seven survivors have been found, according to the ship's owner Maneno Muzuka.
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