The boat smashed into a tree trunk in the rain-swollen River Niger on Tuesday.
"So far 17 bodies have been removed from the water, 12 yesterday (Tuesday) and another five this morning", NEMA coordinator Suleiman Karim told AFP.
Another 17 passengers were rescued by emergency workers and local divers, Karim said.
"We are still searching for at least 26 people because the 60-passenger boat was full at the time of the accident", he said.
The number on board may have been higher as ferries in the riverine region are usually overloaded, Karim said.
The boat had left Jilbabo village in Kebbi state and was heading to Tetebo village in neighbouring Niger state in central Nigeria when the accident happened.
Capsizes are a frequent occurence in Nigeria, where overcrowding is common and unscrupulous operators flout health and safety norms.
The accident rate typically rises in the May-September rainy season when rivers swell.
Last month 74 people were killed in three separate boat capsizes in northern Nigeria, according to emergency services.
In one instance 56 people drowned when an overloaded boat sank carrying 150 passengers in Kebbi state.
The boat was ferrying local traders from neighbouring Niger Republic to a market in Nigeria.