The accident occurred on Friday afternoon near the town of Contah, in the West African nation's Forecariah district, around 100 km (64 miles) southeast of the capital Conakry.
"The boat's passengers were all inside when it capsized. We have counted nine bodies and there are around 30 unaccounted for," Oumar Camara, a resident of Forecariah, told Reuters by phone.
Eighteen people were rescued and survived, he said. Local authorities were continuing to search for victims of the accident as night fell.
Boat wrecks are a fairly common occurrence in West Africa due to lax enforcement of safety regulations and particularly around Forecariah, which is home to a number of villages situated on islands.
The district is located near the border with Sierra Leone. Both countries are struggling to contain the worst Ebola epidemic on record, which has claimed the lives of more than 4,000 people since it was first identified in Guinea in March.
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