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.
Ghosn has become an international fugitive after he revealed on Tuesday he had fled to Lebanon.
He said he did so to escape what he called a “rigged” justice system in Japan, where he faces charges relating to alleged financial crimes.