In April 1943 an RAAF radio station intercepted Japanese messages that they interpreted to indicate that the Japanese military was planning on landing a small force on the Cape York Peninsula. It was thought that the Japanese military may be creating fuel caches for their vehicles, and nearby Australian units were put on alert. After two days of searching for signs of a Japanese landing force, no evidence was found and the search was called off. The rumors of a Japanese landing could easily have continued into modern day and are almost certainly what you are talking about.

Source: Ball, Reg. A., "Torres Strait Force - Cape York, Thursday Island, Merauke 1942 - 1945", Australian Military History Publications, 1996

Late to the party, but there were interviews with (at least one) ex-soldier from the North Australia Observation Unit (NAOU: a.k.a The Nackeroos) soldiers in the Northern Territory who found tracks and evidence of Japanese soldiers having made landfall there although the conclusion reached by the soldier/s interviewed suggested this was most likely in a reconnaissance role only.

Edit: Japanese recon, not Australian.

Source:Richard &​ Helen Walker, "Curtin's Cowboys: Australia's Secret Bush Commandos", Allen &​ Unwin, 1989.