Nigeria's environment watchdog has ordered an inquiry into the apparent disappearance of a UK-registered ship it said had dumped toxic waste.
The watchdog said the Grand America had offloaded containers of electronic waste before disembarking.
But a customs official later said the containers had not been offloaded, and the ship was allowed to leave because no-one had ordered it to be impounded.
Africa, India and China have become favoured destinations for e-waste.
The Grand America was detained at the port about a week ago, together with another ship carrying a similar cargo.
Ngeri Benebo, director general of Nigeria's environmental standards enforcement agency, told the BBC's Focus on Africa programme that the Grand America had arrived at Lagos from Antwerp in Belgium.
She said the other ship, the MV Veradin, was originally from New York and had sailed from Spain.
The MV Veradin is still at the port, but Ms Benebo said she wanted to know why the Grand America was allowed to leave.
Customs spokesman Wale Adeniyi told the programme that officials from the environment agency had inspected the Grand America's cargo last week.
He said it consisted of used TVs, computer monitors and other electronics, and the agency had deemed the cargo toxic.
So the cargo was returned to the vessel and it was allowed to leave, he said.
"There was no detention request received by customs," he said.
The Basel Action Network, a pressure group that monitors the trade in hazardous waste, has raised the alarm about toxic e-waste ending up in Nigeria.
In a recent report the body claimed that about 500 containers with 400,000 second-hand computers were unloaded every month in Lagos ports.