The twin-engine Sikorsky 76C+, operated by the US-based Bristow Group, was heading from an offshore oil rig to the city's international airport on Wednesday when it plunged into the lagoon north of the city.
Four bodies were recovered soon afterwards and six people taken for treatment in Lagos hospitals.
"The last two bodies of the helicopter crash victims have been recovered so, in total, (there are) six people dead and six rescued alive," said Ibrahim Farinloye of the National Emergency Management Agency (NEMA).
Texas-based Bristow's fleet of around 500 helicopters services the global energy industry.
It has operations in Nigeria and most other major regions of the world producing offshore oil and gas.
