Qantas is diverting its planes away from central Sydney to free up space for authorities dealing with the siege in a city cafe.
A Qantas spokeswoman says its flights do not typically pass directly over the CBD, but planes are being diverted from flying over nearby suburbs to leave the way clear for police helicopters and other aircraft.
"We're giving that area a wide berth," she said. The move is expected to have no impact on the airline's flight schedule.
A spokesman for Virgin Australia says its flights are also unaffected at this stage.
"We are monitoring the situation closely. At this stage our operations are unaffected however we will continue to liaise with authorities and security experts," he said in a statement.
A spokesman for deputy prime minister Warren Truss has said the airspace above the CBD remains open although some flights have been re-routed. "The airspace over the Sydney CBD is not in shut down. There are choppers in the air and air traffic is being rerouted according. At this stage no impact on the air traffic network."