The ATR-42 aircraft crashed while carrying 20 passengers and five crew members on a routine mission to Lagos, the nation's economic hub, the air force said on Tuesday.
The plane disappeared from radar and was later found to have crashed close to a naval base in the riverside town of Igbokoda in Ondo state.
Nigerian Aviation Minister Festus Keyamo previously said the aircraft was carrying 32 people.
Officials did not immediately clarify the difference in the two accounts.
Nigerian Chief of the Air Staff Sunday Kelvin Aneke said the accident was "a deeply painful moment for the Nigerian Air Force and the nation" and assured the bereaved families of the agency's full support.
Nigerian President Bola Tinubu declared three days of mourning and directed flags to be lowered throughout the country to mourn the victims.
"I have directed the Nigerian Air Force to immediately commence a thorough investigation into the cause of the crash to prevent future occurrences," Tinubu said in a statement.
The extent of the damage and cause of the accident remained unclear on Tuesday.
The ATR-42 is often used by the Nigerian military for intelligence, surveillance and reconnaissance and for transporting personnel and supplies.
Residents told The Associated Press the aircraft crashed near a river and was partially sinking in the water.
Videos posted online that appeared to be from the accident scene showed people gathered by a river as rescuers attempted to reach the area.
10°C