The use of the back-up system raises questions about the reliability of the new baggage system, which was plagued by a software glitches prior to the Games.
According to officials, the back-up system, known as Pier Tag, has been introduced to allow off-airport baggage processing at the Olympic Athletes Village.
Sydney Airport's International Terminal is expecting to process 44,000 passengers on Monday, including athletes and nearly 7000 Olympic Family members. Sydney Airport Corporation (SACL) is estimating each athlete will have at least six pieces of luggage.
Despite reports the system is manually operated, Eric Aubert, from Sydney Airport public affairs, said Pier Tag is the electronic permanent back-up component of the main system.
"It is a low-level information, fully electronic, fully automated system," Aubert said.
"It is just as efficient as the main system."
According to Aubert, the difference between the Pier Tag system and the main system is the level of information contained on the computerised tag.
Using the Pier Tag system means in the case of transfers, luggage will have to be manually sorted before travelling to a third airport, Aubert said.
"It is because of the low level of information on the bag tags," he said, adding that only around 20 per cent of baggage will be affected by the manual process.
SACL has worked in consultation with other airports to run the system that has been operating at Sydney Airport over the past week to familiarise staff and airlines with the procedures. It will be used off-site for the first time during the Games on Sunday.
Rather than running two systems in conjunction, SACL opted to use only the Pier Tag system to "reduce confusion and complexity", Aubert said.
"With the very high loads there could be problems running two different systems," he said.
Aubert said despite the differences, the Pier Tag system was not expected to cause delays. By using an off-site process, SACL is hoping to reduce the pressure and load on the baggage system at the airport.
"It's quite the reverse. It will reduce the likelihood of delays," he said.
"We have done it to ease the pressure and speed up the [baggage check-in] process for the Olympic Family and athletes."
Athletes will check their luggage in and obtain their boarding passes at the village using portable scanners. The baggage will be security checked and loaded onto trucks to be transported to Sydney Airport. Baggage for early morning flights will be processed as normal in the terminal between the airport's non-operating hours 11:30pm until 4:30am. Baggage arriving throughout the day will be loaded onto aircraft immediately to ease the strain on the internal baggage system.