By Mr Adesina Tiamiyu, the General Manager, Lagos State Emergency Management Agency, said that the incident happened on Wednesday at 8:20pm.
Tiamiyu said that the rescue team were still searching for five other missing passengers.
The boat which was en route Ojo from Liverpool capsized few minutes after take-off.
He said: ”12 of the passengers were rescued alive by the Lagos State Waterways Authority officials and local divers.
”Two males and one female were confirmed dead, while search and rescue operation have been put on hold till the following day for the remaining five missing people.
”The three bodies have been bagged, and the men were handed over to the State Environmental Health Monitoring Unit to be deposited at the morgue.
”The female victim, identified as Alhaja, was handed over to her family after proper documentation by the Marine Police Officers,” Tiamiyu said. NAN