Suharto proffered a strongly anti-Communist stance during his early reign, a position that found great support with successive Australian Government.
The Gough Whitlam-led Australian government apparently denied knowledge of the killings,[5] and instead maintained support for Indonesia's annexation of East Timor.
Paul Keating became Prime Minister in 1991, and was noted as a fervent supporter of stronger diplomatic ties between the two countries.
"[11]It was in 1994 that Keating first proposed an official security agreement between the two nations, raising the point with President Suharto in June of that year.
[9][13] The treaty begins with a preamble that addresses the mutual desire of both nations to reinforce the bond between them while working together to maintain peace and stability in the Oceanic and South-East Asian regions.
"As a result, in September 1999, the same month Australia entered East Timor, Indonesia officially abrogated 1995 agreement.
However, two occasions allowed for the restoration of strong political ties between Australia and Indonesia prior to the signing of the Lombok Treaty in 2006 - the Bali Bombings in 2002, and the Sixth Indonesia-Australia Ministerial Forum in 2003.
[20] This treaty was much more substantial than the earlier 1995 Agreement, and dealt more explicitly with the exact security issues each nation would face.
Then, the treaty goes into the articles proper, as in the earlier agreement: The first article simply outlines the purpose of the treaty, as way to both provide a framework for cooperative security regarding common security threats to the two nations; and to establish a mechanism by which the two nations may continuously interact when aforementioned threats arise.
'[23] Additionally, he draws parallels between the 2005 West Papuan conflict and the 1999 East Timor crisis - both involved Indonesian territories inciting some separatist action against Indonesia.
Additionally, judging by Elmslie's words and context surrounding the abrogation of the 1995 Agreement, that clause 2.3 was also influenced by Australia's protracted involvement in and direct conflict with Indonesia during the 1999 East Timor Crisis.
[25][27] The two Australia-Indonesia Defence Cooperation Arrangements (DCA) exist to reinforce the Lombok Treaty, and both act as reaffirmations of the commitments laid out in 2006.
Instead, the Joint Understanding acted as a set of rules both nations would agree to follow in accordance with the Lombok Treaty.
It was believed the Joint Understanding came about as a result of a 2013 investigation that revealed espionage activities carried out by Australia in 2009, targeting then-Indonesian President Susilo Bambang Yudhoyono,[29] as the agreement features the clause: "the Parties will not use any of their intelligence, including surveillance capacities, or other resources, in ways that would harm the interests of the Parties".
[30] The treaty-level agreement will allow for enhanced practical cooperation and interoperability between two armed forces in areas such as maritime security, counter terrorism, humanitarian and disaster relief, logistics support, education and training, as well as across defence industry, and would help prevent future security threats in the Asia-Pacific region through collaborative efforts to maintain peace and stability.