The boat met "hostile weather", Alex Koroma, a station manager for Radio Kolenten, told the AFP news agency by telephone.
The vessel, named Amunafa, is powered by outboard motors and regularly ferries goods and people between Sierra Leone's coastal towns and villages.
Gabi Menezes, Al Jazeera's correspondent in Freetown, said the severe conditions appeared to contribute to the disaster.
"It is the rainy season in West Afrca and accidents like this are not uncommon during heavy rain storms… it is not yet clear whether the boat was a ferry or a dug-out canoe, which carry over a hundred people," she said.
"If it was a canoe it is not surprising – they are often overloaded and very badly policed."