The gold ingots, valued at approximately €1.5 million, were in the possession of the Brink’s secure transportation company, and destined to travel in the hold of an Air France flight from Paris to Zurich on September 19th, according to TF1 television.
Air France said on Tuesday it had filed a complaint with police.
"We hope the investigations will allow us to quickly determine the sequence of events and identify those responsible," a spokesman said.
Brink's a US-based company, which regularly transports gold to Swiss banks as funds transfers, had put nine suitcases, containing roughly 300 kilos of gold ingots, on the flight from Charles de Gaulle airport last Thursday.
On arrival in the Swiss city, two cases were missing from the Brink’s delivery, containing a total of 44 kilos of gold bars.
However in a statement on Tuesday Brink's denied any reponsibility over the missing gold bars, saying "it was not in charge of the transport and the packages were not under its responsibility when they disappeared."
The company added that its task "was limited to ensure the safety of the consignment during its transit at Charles de Gaulle," a mission that Brink's claimed it carried out "perfectly well".
The French subsidiary of Brink's employs a total of 6,000 people in France. It has 1,800 security officers who work in French airports to inspect passengers and baggage.
France's national aviation police, the GTA, is leading the investigation into how the missing packages were taken from the aircraft, and by whom.
Cocaine seizure in Paris
The presumed theft comes at a bad time for Air France chiefs.
Air France staff are already in the spotlight, after the recent record seizure of 1.3 tonnes of pure cocaine, found in 30 suitcases on an Air France flight from Caracas to Paris.
The €200 million ($270 million) haul has so far led to the arrest of nine people, including three Venezuelan security agents. Three British nationals are believed to be among six people arrested in Paris, although French authorities are yet to confirm these reports.
Miguel Rodriguez, Interior Minister in the South American country, told AFP it was highly likely the smugglers had accomplices within Air France working with them.
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"How can the cocaine shipment reach France and it gets taken out without going through the normal controls?" he asked.
For his part, aviation security expert Christophe Naudin said the smuggling had to be an Air France inside job to some extent, given how the suitcases appear to have been loaded onto the plane without going through the normal check-in procedures.
"By definition there must have been help from people inside Air France's operation in Caracas to get the bags labelled," Naudin said.
The airline has ordered an internal investigation into the cocaine seizure, and says it is working closely with the police over the incident.