The deportees,who are all male, were brought back in a chartered aircraft with registration number EL-SMU/3737.
Joseph Alabi, spokesman of the Lagos airport police command, confirmed the development to NAN.
Alabi said 39 of the deportees were alleged to have committed immigration-related offences while one of them was allegedly involved in drug dealing.
He said the deportees were received by officers of the Nigerian Immigration Service (NIS) , the National Agency for the Prohibition of Trafficking in Persons (NAPTIP) and the police.
Also on ground to receive them were officials the Federal Airports Authority of Nigeria (FAAN) and the National Drug Law Enforcement Agency (NDLEA).
They were profiled by immigration authorities while those without serious charges were allowed to depart to their various destinations.
This is the third time the Italian government has expelled Nigerians in less than two months.