[2][3] Cold War security concerns were emphasised,[4] while foreign powers also placed high importance on good relations with Indonesia and were largely reluctant to assist a push for independence as a result.

[5] In late 1998, the Australian prime minister, John Howard, with his foreign minister, Alexander Downer, drafted a letter to Habibie supporting the idea of autonomy but incorporating a suggestion that the long-term issue of East Timorese self-determination could best be defused by providing the East Timorese with an opportunity for a plebiscite after a substantial period of autonomy.

[6] The letter upset Habibie, who saw it as implying Indonesia was a "colonial power", and he decided in response to announce a snap referendum to be conducted within six months.

After the result was announced on 4 September, violent clashes, instigated by a suspected anti-independence militia, sparked a humanitarian and security crisis in the region, with Xanana Gusmão calling for a UN peacekeeping force the same day.

[1] On 6 September, Operation Spitfire commenced with Royal Australian Air Force (RAAF) C-130 Hercules aircraft evacuating UNAMET staff, foreign nationals and refugees, including Bishop Belo, to Darwin from Dili and Baucau airfields with protection provided by unarmed Special Air Service Regiment (SASR) soldiers.

Australia's Opposition Spokesman on Foreign Affairs, Laurie Brereton, was vocal in highlighting evidence of the Indonesian military's involvement in pro-integrationist violence and advocated United Nations peacekeeping to support the East Timor's ballot.

[9] The Catholic Church in Australia urged the Australian Government to send an armed peacekeeping force to East Timor to end the violence.

[11][12] The Australian prime minister, John Howard, gained the support of United Nations Secretary-General Kofi Annan and U.S. President Bill Clinton for an Australian-led international peacekeeping force to enter East Timor to end the violence.

On 12 September, Clinton announced:[13] [T]he Indonesian military has aided and abetted militia violence in East Timor, in violation of the commitment of its leaders to the international community.

This has allowed the militias to murder innocent people, to send thousands fleeing for their lives, to attack the United Nations compound.

They must permit humanitarian assistance and let the U.N. mission do its job ... We are ready to support an effort led by Australia to mobilize a multinational force to help to bring security to East Timor under U.N. auspice ... the eyes of the world are on that tiny place and on those poor innocent, suffering people.

Australia was the single largest provider, with 14 ships deployed with INTERFET between 19 September 1999 and 23 February 2000: the frigates Adelaide, Anzac, Darwin, Sydney, Newcastle, and Melbourne; the landing ship Tobruk, the landing craft Balikpapan, Brunei, Labuan, Tarakan, and Betano; the fast transport Jervis Bay; and the replenishment vessel Success.

Led by Australia, who contributed 5,500 personnel and the force commander, Major General Peter Cosgrove, it was tasked with restoring peace and security, protecting and supporting UNAMET, and facilitating humanitarian assistance.

Other force level troops included military police, an intelligence company, an electronic warfare squadron, elements of an artillery locating battery, and topographic survey personnel.

[27] Most United Nations Mission in East Timor (UNAMET) personnel had already been evacuated from the region in the preceding months by the Royal Australian Air Force, although a small number had remained behind.

[28] With the withdrawal of the Indonesian forces and officials, UNAMET re-established its headquarters in Dili on 28 September and on 19 October 1999, Indonesia formally recognised the result of the independence referendum.

[34] West Force (WESTFOR) consisting of 2RAR, 3RAR, and 1RNZIR, in addition to supporting aviation, engineer and armoured units, was tasked with securing the border region.

[37] Later, intelligence reports speculated on the involvement of Indonesian military personnel in the attempt to cut off and destroy the Australians, whilst conjecture as to the identity of the pro-Indonesian militias and the source of their arms and training increased in the media.

[43][42][44] The night before Australian Navy Clearance divers from HMAS Success had conducted a clandestine beach reconnaissance of the amphibious landing area.

[49] On 28 February 2000, INTERFET handed over command of military operations to United Nations Transitional Administration in East Timor (UNTAET).

[34] A New Zealand soldier, Private Leonard Manning, was shot dead during a contact on 24 July 2000, becoming the first combat fatality since the United Nations-backed forces had arrived in September.

[58] Australia was refused US ground troops but was able to secure vital support for airlift, logistics, specialised intelligence, over the horizon deterrence, and "diplomatic muscle".

[61] A Force Logistic Support Group was deployed during October and November based on the 10th Force Support Battalion (10 FSB), which included supply, transport, port operators, water transport and maintenance personnel, while a forward surgical team, preventative medical section, signals squadron, and engineers from the 17th Construction Squadron and a section of the 19th Chief Engineer Works were also attached.

Reductions in defence spending over the previous decade had led to the run down of its logistic support force, resulting in the requirement to quickly implement a range of ad hoc measures to overcome these shortfalls.