The Daily Telegraph reported two masked men, one armed with a handgun, demanded money at the Swiss Grand Resort and Spa at Bondi Beach before fleeing in a waiting car.
Swan and Thomas, on a short break for the Australia Day long weekend, returned to the hotel 45 minutes later to find police already in attendance.
The Daily Telegraph photographed the pair at the entrance to the hotel, and claimed Swan used an orange traffic cone as a megaphone to yell at passing cars.
But Brownlow Medalist Swan was quick to refute that on Twitter on Monday.
For the record I was no where near an orange traffic cone all night. #mistakenidentity #noabuseyelled and I did not rob the hotel either
— Dane Swan (@swandane) January 28, 2013
Police allowed Swan, Thomas, and the two women that accompanied them to return to their rooms.
According to police, the bandits threatened the hotel's manager and then a security officer with the gun, before demanding the safe be opened.
Police said the bandits fled with "a large sum of cash", before jumping into a car.