He said there were 39 survivors.
With no manifest of the passengers on board, the number missing is an estimate based on the capacity of the boat, he said.
The vessel was actually nine traditional wooden canoes, known as pirogues, all tied together, Magbado said.
He added that the accident may have been caused by "overcrowding aggravated by bad weather" during the night.
The scale of the accident was not clear until it was reported by media late on Friday, and confirmed on Saturday by provincial authorities.
Magbado said the Mongala authorities had informed Kinshasa of the sinking just after it occurred, but had waited for more information about the number of casualties.
Search and rescue operations are continuing, but hopes are fading of finding more survivors, he said.
Provincial authorities have declared three days of mourning from Monday.