Considering that indonesia can barely field a capable military and the
rest in SE asia have small militaries, who are these cruise missiles
directed against

China perhaps? Could it be in response to countries in the region buying
Su-27/30 long range strike planes?

My guess is that US arms merchants are looking to do brisk business in SE
Asia but not finding any opportunities. So get australia to start an arms
race in the region (?)

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Australian cruise missile plan

http://www.spacewar.com/2004/040826052722.z4dkcg5c.html