Ex-Nissan boss Carlos Ghosn used two of a private Turkish company's planes illegally in his escape from Japan.
According to Reuters, MNG Jet says an employee falsified lease records to exclude Ghosn's name from the documents.
MNG Jet said it had filed a criminal complaint over the incident.
The news comes a day after Turkish police detained seven people, including four pilots.
They're investigating Ghosn’s passage through Istanbul en route to Lebanon.