The Air France flight was traveling from Paris to Zurich with the gold on board. Around 44 kilos of gold bars, worth €1.5m, are believed to have disappeared from the plane's hold.
The latest theft comes amongst suspicions that Air France staff were complicit in a recent €200 million cocaine smuggling operation.
According to TF1 television (French language), the gold bars were in the possession of the Brink’s secure transportation company, and were destined to travel in the hold of an Air France flight from Paris to Zurich on September 19th.
RT reports that Brink's is a US-based company and regularly transports gold to Swiss banks as funds transfers. They had apparently placed nine suitcases, containing around 300 kilos of gold ingots, on the flight from Charles de Gaulle airport last Thursday.
However, on arrival in Zurich, two cases were missing from the consignment, containing a total of 44 kilos of gold bars.
Brink's said in a statement on Tuesday that they denied any responsibility over the missing golf bars, stating, "it was not in charge of the transport and the packages were not under its responsibility when they disappeared."
Adding that the company's 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".
Air France said in a statement on Tuesday that it had filed a complaint with the police.
"We hope the investigations will allow us to quickly determine the sequence of events and identify those responsible," a spokesman said.
France's national aviation police, the GTA, is now leading the investigation into how the missing packages were taken from the aircraft, and by whom.
Reportedly the French subsidiary of Brink's employs a total of 6,000 people in France and has 1,800 security officers working in French airports, inspecting both passengers and baggage.
The loss or theft of the gold comes at the wrong time for Air France chiefs, as the airline is 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 haul, worth €200 million ($270 million), has so far led to the arrest of nine people, including three Venezuelan security agents.
Three UK nationals are believed to also be among six people arrested in Paris, although this is still to be confirmed by French authorities.
The Interior Minister of Venezuela, Miguel Rodriguez, told AFP it was highly likely the smugglers had accomplices within Air France working with them.
"How can the cocaine shipment reach France and it gets taken out without going through the normal controls?" he asked.
Aviation security expert, Christophe Naudin also said the smuggling had to be an Air France inside job to some extent, as the suitcases appeared 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.
Air France has apparently ordered an internal investigation into the cocaine discovery and seizure, and reports that it is working closely with the police over the incident.