The ability to use watercraft was not developed in very early humans. Therefore, archaic Homo Sapiens could not have taken advantage of this in order to get to islands such as those of Australia or Java. However, there is considerable debate as to how humans arrived to these regions.
The most likely answer is that humans arrived to many of these regions during the closing stages of the Pleistocene. During this time period, glaciation was common, which led to particularly low sea levels. These connected many territories that are now separate (such as New Guinea and Tasmania, which were connected to Australia). It also meant that islands were much closer to each other. Early humans appeared to have reached these areas through "island hopping." It is also possible that these movements were accidental, as a result of tsunamis and other natural events.