Investors behind the airline have struggled to deal with $250m (Â£157m) of debt taken on when they bought the carrier from Virgin two years ago.
In June, Air Nigeria was grounded by regulators amid safety concerns.
If the airline can resolve its debt problems, it could yet return to the skies, analysts said.
The grounding of services by the country's aviation regulator followed a crash in June, involving a jet operated by Dana Air, which smashed into an apartment block in Lagos, killing 163 people.
Although an investigation into the crash is still ongoing, Dana has been given permission to start flying again.
Last week, the global air transport body IATA said the most pressing problem for African aviation is safety, with the continent's record of accidents nine times the worse than the global average.
The demise of Air Nigeria leaves the country with just four domestic carriers operating scheduled flights, a blow for efforts to develop the country's economy.
According to IATA, African aviation supports seven million jobs and business activity worth nearly $68bn.
Meanwhile, Nigeria's government is considering a strategy to create another national carrier.
Air Nigeria will make its final long-haul flights on Monday after announcing the suspension of all services and laying off 800 staff last week.