Totally, 39 passengers were on board the boat and the remaining 26 have been rescued.
The operation has been complicated by the fact that the boat capsized in the Shiroro area where armed gangs have control, according to the rescue service.
Very few people can get there due to the bandit activity in the area, says spokesperson Ibrahim Hussaini.
Armed gangs, called "bandits", are establishing themselves to an increasing extent in the Nigerian countryside. Poverty and lack of government presence are believed to be behind the growing problem. The gangs attack, plunder and burn villages, demand "tax" and carry out kidnappings for ransom.
Sunday's capsizing is the latest in a series of fatal boat accidents on Nigerian waters, last year at least 326 people died. The accidents are mainly common in remote communities during the country's rainy season, due to overloaded and poorly maintained boats.