"Fourteen school children were aboard the boat when it overturned," Ibrahim Farinloye of the National Emergency Management Agency (NEMA) told AFP.
"Eight of them were rescued alive. We recovered three corpses yesterday (Wednesday) and three more today, bringing the total death toll to six."
The tragedy occurred in the Irawe western district of the oceanside city on Wednesday when the boat lost control and upturned, he said.
Many communities and residents on islands in Lagos and other parts of the country commute to work, school and markets daily on water, in some cases to avoid monster traffic jams.