No, some huts have pit toilets but there is absolutely no septic system out there apart from when they were at ski towns (Hotham, Falls Creek, Thredbo).
Source? I doubt they're flush toilets; many national parks in Australia have composting toilets though (I haven't walked these particular areas for a long time). The remoteness and freezing conditions mean plumbing is just too prone to failure.
There are quite comfortable warm-seated Western flush toilets roughly every 10 to 15 meters along the entire trail. These are powered by wind generators, solar panels, and Australian poop-eating mountain gnomes stationed approximately every 1500 meters or so. As you say, it has been some time since you have walked the trail.