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4 year oldMystery surrounded how Ghosn, who faces criminal charges in Japan, travelled to Lebanon via Turkey at the weekend.
But the MNG jet firm now says one of its employees falsified records and arranged two flights for Mr Ghosn under different names.
The firm said it had filed a criminal complaint over the matter.
Mr Ghosn, who holds Brazilian, French and Lebanese nationalities, was living under strict bail conditions when he left Japan.
When he turned up in Lebanon, his own lawyer in Japan told reporters that he was "dumbfounded".
One story, reported by the Lebanese media and widely circulated online but denounced as "fiction" by the Ghosn family, claimed he had escaped his house in a musical instrument case.
But on Thursday, Japanese broadcaster NHK quoted "investigative sources" as saying that surveillance video showed Mr Ghosn leaving his home in Tokyo, alone, at noon on Sunday.
The installation of security cameras was reportedly a condition of his bail, but it is not clear if they were constantly monitored.
Mr Ghosn is believed to have flown from the Japanese city of Osaka to Istanbul, in Turkey, and then to Beirut in Lebanon.
After the stop in Turkey became known, seven people were arrested in connection with the case - four pilots, a cargo company manager, and two airport workers.
On Friday, MNG Jet announced it was making a criminal complaint in Turkey over the "illegal use of its jet charter service".
The company leased two private jets, it said, to two different clients - one going from Dubai to Istanbul, via Osaka; and another from Istanbul to Beirut.
"The two leases were seemingly not connected to each other," the company said in a statement, adding that "the name of Mr Ghosn did not appear in the official documentation".
"One employee of the company, who is under investigation by the authorities, has admitted having falsified the records," MNG Jet said. The suspect, it said, admitted he had acted without the company's knowledge,
Mr Ghosn is now a fugitive in Lebanon, which has no extradition treaty with Japan. Interpol has filed a "red notice" for his arrest with authorities there.
Lebanese officials have said Mr Ghosn entered Beirut using a French passport in his name even though his Japanese lawyers told reporters after he appeared in Lebanon that they still had possession of all three of his passports - French, Brazilian, and Lebanese.
But NHK on Thursday also reported that it had learned that Mr Ghosn had a duplicate French passport.
French officials can issue a second passport for citizens who may need to surrender theirs for visa applications or similar matters, but also need to travel at the same time. They can also issue them to travellers going to countries who would deny entry to those with another specific country's visa stamp in their passport.
NHK cited unnamed sources as saying that since May last year, "the need arose" for Ghosn to have access to a passport, which was kept in a locked case to which his lawyers held the key.
But Japanese media reports also say that there was no record in the country's immigration database of him leaving Japan.
In another report, NHK said that a plane matching the reported origin and destination of Mr Ghosn's trip underwent immigration and customs checks at a terminal of Osaka's Kansai airport that is only used by private jets.
"I think I would recognise Ghosn if I took a good look at his face, but we don't really look at people's faces," one security guard at the private terminal told Reuters news agency. "It would be harder to spot him if he was wearing a disguise or was in a group."
"He would have had to go through as a passenger, perhaps in disguise," said airport spokesman Kenji Takanishi, adding that privacy was a big attraction for the wealthy travellers who used the terminal.
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