Indonesia-Australia relations are entering an unprecedented phase of formalised security cooperation, marked by a watershed Treaty on Common Security set for signing in early 2026. Regardless of how closely both governments are now deepening their cooperation, Papua remains a sensitive point for the two nations that, if left unaddressed, could undermine the durability of this emerging security architecture.
Modern Indonesia-Australia ties have oscillated between cooperation and suspicion, often hinging on questions of sovereignty. The first formal bilateral security agreement — the 1995 Agreement on Maintaining Security — was a breakthrough, committing both sides to consult on mutual security interests. But this pact collapsed in 1999 when an Australia-led UN peacekeeping force entered East Timor as it voted for independence. A decade later, both countries sought to rebuild ties through the 2006 Lombok Treaty, which explicitly reaffirmed Indonesia’s sovereignty and territorial integrity, specifically over Papua. Despite these assurances, bilateral relations came under strain again in 2013 after revelations that Australian intelligence had tapped senior Indonesian officials, including then-President Yudhoyono, before being restored through a Joint Understanding on a Code of Conduct for intelligence matters in August 2014.
The current Australia-Indonesia Treaty on Common Security, which represents a significant upgrade over earlier iterations, outlines commitments to consult each other if either is threatened, and to hold regular security dialogues at the leader and ministerial levels. It deliberately stops short of a mutual defence pact — respecting Indonesia’s non-alignment posture — but symbolically elevates the partnership to its highest level ever. Interestingly, this pact comes on the heels of Australia’s Pukpuk Treaty with Papua New Guinea (PNG) in mid-September 2025 — PNG’s first alliance and Australia’s first new defence treaty since ANZUS. This formal mutual defence arrangement underscored Canberra’s strategic focus on its northern approaches amid Beijing’s growing influence in the Pacific.
On the sidelines, however, some Indonesian elites likely see the Pukpuk Treaty as a response to Jakarta’s increasing strategic ties with China and to reports that Russia had informally sought basing access at Biak in Papua province. Though the Australian and PNG counterparts consulted Indonesia before signing, the sense of strategic signalling persists.
Fortunately, the establishment of the Indonesia-PNG-Australia Trilateral Defence Ministers’ Meeting in December 2025 offers a direct mechanism to enhance cooperation in areas of mutual interest. Complemented by the Indonesia-PNG Defence Cooperation Agreement, specifically its focus on border management, these arrangements may help further ease sensitivities among the three countries.
Australia may have no territorial claim in Papua, but instability there would directly affect its northern approaches and test Canberra’s new mutual defence commitments under the Pukpuk Treaty. And any perceived future presence of Russian or Chinese influence in Eastern Indonesia, even if framed as cooperation with Jakarta, would alter the regional balance in ways Canberra cannot afford to ignore.
Traditionally, West Papua is precisely the issue that Canberra and Jakarta avoid discussing in any institutional context. For Indonesia, Papua, comprising its restive easternmost provinces, is an internal issue of territorial integrity, non-negotiable and sensitive to the core. But for many Australians, Papua has long been viewed through a human rights and self-determination lens, even as their governments tread cautiously on the issue. Canberra’s perceived sympathy for West Papuan separatism has long irritated Indonesian policymakers. This was evident in January 2017, when “insulting” training materials at an Australian base appeared to question Indonesia’s sovereignty over Papua and demean the country’s five founding principles of Pancasila, prompting a brief but sharp downturn in their relations. This demonstrated that Papua must be part of any Indonesia-Australia security framework, because it is the issue most likely to trigger miscalculation if left unaddressed.
This risk is not hypothetical. In mid-January 2026, armed separatists of the Free Papua Movement fired shots to intimidate Freeport Indonesia workers while surrounding them at a company outpost in Central Papua, prompting a high-risk rescue operation by Indonesian security forces. The incident shows how Papua’s volatile security environment can escalate rapidly, with implications that extend to Indonesia’s eastern neighbours.
Indonesia’s approach to Papua, and what it expects from Australia, is now evolving under President Prabowo. The ex-general has made no secret of his desire to bolster Indonesia’s military might across the archipelago, notably its Eastern region. His administration, which includes hardliners, has so far continued a security-heavy approach in combating West Papuan rebellion. In August 2025, Prabowo launched six new regional military commands to strengthen its defence posture by extending territorial reach and deploying forces to key strategic areas amid global instability. One of these new commands is based in Merauke, South Papua — establishing a whole army division headquarters in a province adjacent to PNG. Alongside this, Indonesia is beefing up its air and naval presence in its eastern waters.
What Indonesia’s Prabowo might want from Australia’s Albanese regarding Papua sits alongside Australia’s own specific expectations of Indonesia vis-à-vis Papua.
Jakarta will likely demand explicit respect for Indonesia’s territorial integrity and firm reassurance of non-interference in Papuan matters in every possible aspect. At the same time, Indonesia will likely make it clear to Australia that it intends to engage with all major actors, since the treaty is partly designed to allow Prabowo to demonstrate that he can balance relations with both U.S.- and China-aligned partners.
Concurrently, Australia’s 2024 National Defence Strategy adopted a posture of “deterrence by denial” to prevent hostile power projection near its northern approaches rather than relying solely on coalition support. Prabowo’s appearances alongside non-Western leaders during the 2025 China Victory Day Parade have likely sharpened Australian concerns that Indonesia might edge closer to a China-led CRINK Axis that seeks to challenge U.S. hegemony in the global order. The priority for Canberra is hence to secure transparency regarding any foreign presence or strategic involvement, specifically from nations of the so-called Axis of Upheaval, in Indonesia’s Eastern region. Australia will expect any developments to be communicated clearly under the new treaty’s consultative framework.
As Southeast Asia’s natural leader and the Pacific’s principal security actor, Indonesia and Australia, respectively, carry a special responsibility for regional stability within an architecture of collaboration that, if successful, could anchor regional security in an era of great-power uncertainty. But this architecture must be comprehensive — and that means institutionalising trust exactly where distrust has historically run deepest.
Geo Dzakwan Arshali is undergraduate student in International Affairs Management at School of International Studies, Universiti Utara Malaysia, and Research Intern (Regional Security Architecture Programme) with Institute of Defence and Strategic Studies (IDSS) at S. Rajaratnam School of International Studies (RSIS). He is concurrently an Emerging Leaders Fellow at FACTS Asia, Cadet Researcher (Outgoing) at Asian Institute of International Affairs and Diplomacy (AIIAD), and Senior Analyst & Program Manager at World Order Lab.
Alfath Aziz Kurnia is an undergraduate student in International Affairs Management at the School of International Studies, Universiti Utara Malaysia. He is currently an undergraduate researcher at the Asian Institute of International Affairs and Diplomacy (AIIAD) and a Content Writer at World Order Lab. His research interests focus on war studies and international security, with particular attention to Southeast Asia’s relations with external powers and regional maritime security issues.
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