The helicopter, operated by the US-based Bristow Group, came down behind a police station in the Oworonshoki area in the north of the city, according to the National Emergency Management Agency.
"Four dead bodies (have been) recovered so far," said NEMA spokesman Ibrahim Farinloye, adding that the wounded had been taken to two hospitals, where their condition was not immediately clear.
A witness told Channels TV news station the helicopter made a loud noise before nose-diving into the water near the 12-kilometre (seven-mile) Third Mainland Bridge, the longest of three bridges connecting Lagos Island to the mainland.
There have been several military helicopter accidents across Nigeria in recent years, but air crashes involving private choppers have been relatively rare.
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