Here is a link to the full text of the above agreement http://www.dfat.gov.au/geo/indonesia/ind-aus-sec06.html
Read on for some selected quotes
"3. The Parties, consistent with their respective domestic laws and international obligations, shall not in any manner support or participate in activities by any person or entity which constitutes a threat to the stability, sovereignty or territorial integrity of the other Party, including by those who seek to use its territory for encouraging or committing such activities, including separatism, in the territory of the other Party;"
Defence Cooperation
In recognition of the long-term mutual benefit of the closest professional cooperation between their Defence Forces,
1. Regular consultation on defence and security issues of common concern; and on their respective defence policies;
2. Promotion of development and capacity building of defence institutions and armed forces of both Parties including through military education and training, exercises, study visits and exchanges, application of scientific methods to support capacity building and management and other related mutually beneficial activities;
3. Facilitating cooperation in the field of mutually beneficial defence technologies and capabilities, including joint design, development, production, marketing and transfer of technology as well as developing mutually agreed joint projects.
Intelligence Cooperation
12.Cooperation and exchange of information and intelligence on security issues between relevant institutions and agencies, in compliance with their respective national legislation and within the limits of their responsibility.