"As of now, we have lost 42 and 100 are missing," he said of the Friday evening disaster.
Rescue teams were on site, searching the waters for further bodies after what Shaba described as the worst accident to hit the state in recent years.
"We are going to learn a lesson from this," he told AFP.
According to Shaba, the vessel was packed with far too many traders as well as the goods they acquired after leaving a market in Malilli.
While he blamed "overloading" as the primary cause, he also said that high waters on the Niger could have been a contributing factor, following a heavy rainy season in the area.
Nigeria has seen significant flooding in regions across the country in recent years.
Passenger boats, especially in more remote areas, are often poorly maintained.
Operators typically try to cram on board an excessive number of passengers to boost income.