Passenger flights into the country, with the exception of ones to evacuate people or repatriate Nigerian citizens, have been banned for weeks. The ban will remain in place until at least June 4.
Flights for essential services, such as the delivery of food supplies and items for humanitarian use, are permitted.
Aviation Minister Hadi Sirika said in a tweet on Sunday that a plane had been impounded after the rules were broken.
Sirika said a UK company "was given approval for humanitarian operations but regrettably we caught them conducting commercial flights."
The message added: "The craft is impounded, crew being interrogated. There shall be maximum penalty."
James Oduadu, an aviation ministry spokesman, told Reuters later in a telephone interview that the plane was operated by a company called FlairJet.
Representatives of FlairJet, a British private charter company that is an affiliate of Flexjet, did not respond to emails and a phone call seeking comment.