"The corpse, whose identity is yet to be ascertained, has been deposited at an undisclosed mortuary," Yakubu Dati, of the Federal Airports Authority of Nigeria (FAAN), said in a statement.
The man's body was discovered in the wheel compartment of the Arik Air plane on Saturday at Lagos' international airport, as ground staff prepared the jet for another flight to New York, he added.
"FAAN is currently reviewing footages of the CCTV system and airside security operations with a view to identifying the gaps and personnel failure, if any, in order to take remedial actions," he said.
There was no immediate response from Arik Air when contacted by AFP but the private airline's spokesman confirmed the incident in local media.
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"Arik Air engineers were checking the aircraft in preparation for a flight when the body of the stowaway was discovered in the main wheel well of the aircraft," said Adebanji Ola in a statement.
"Investigations are still on to determine where the stowaway originated," he said, adding that the aircraft, an Airbus A345-500, was fumigated.