Take this with a grain of salt, because a quick google can't find the sources I was looking for, and so this is based of memory of two papers I wrote in 2001... Although if you are looking for the Australian angle, Damien Kingsbury, Scott Burchill, Hugh White and Robert Mann have all written articles on this in the past...

Anyway, both Howard (Australia's PM) and Habibie did not support any sort of referendum or independence, but after growing protest movements throughout Australia (I was at one of the main ones in Melbourne, where Xanana Gusmao spoke to the crowd of several thousand people, from his Jakarta prison cell), in one of only a handful of changes of this kind, Howard made a decision to follow public opinion...

Howard sent a very strongly worded letter to Habibie saying this (its worth noting that we trained the Indonesian special forces Kopassus who did most of the damage, and our most progressive government ever green lighted the invasion), and Habibie went kind of half way.

What happened next was very interesting, a campaign of terror led by Kopassus against the yes vote, and Australia refused to send in peace keepers, eventually the yes vote prevailed, and Australia sent in troops... Here, we clashed directly with Kopassus, and with their militias, but only after the fact in a sense...

But just as interesting, is that Australia committed so many troops to East Timor that we asked America to "provide cover" and so during our initial deployment, the US moved an aircraft carrier into the region.

So broadly speaking, the US backed our commitment - although they, along with many others - criticised the decision to wait, which allowed for the No Vote campaign of terror...