There was contact and trade.

Before the colonial period, coastal regions of what is now the Indonesian provinces of Papua and West Papua were connected with other parts of the archipelago by trade and empire. In the ~14th century the Majahapit, based in Java, had tributaries across the archipelago, including in Papua. In the following centuries, the Sultanate of Tidore similarly claimed territory in Papua. During the colonial period, most of the same shipping routes would've remained, albeit under (predominantly) Dutch rule.

More broadly, ships, goods and people from the major trading hubs across the archipelago in some cases moved all over the archipelago and beyond. Therefore, in the port cities at least, significant contact between different cultures went on regardless of whom the ruling power(s) might've been at the time. One notable illustration of this is Bugis Street in Singapore, once a red light district popular with sailors and named for the Bugis, a prominent seafaring culture who hail from South Sulawesi thousands of miles away.

Australia is further away and Northern Australia to this day is sparsely populated. Boats, predominantly from South Sulawesi, harvested trepang (sea cucumber) in coastal parts of what are now the northernmost parts of Western Australia and the Northern Territory for at least a few hundred years, commencing at least as early as the early 18th century. Marriages between trepangers and Aboriginal Australians were not unheard of, and there is evidence of Yolgnu (from East Arnhem Land) accompanying trepangers back to Makassar. This industry died off soon after Australian Federation in 1901.