Under the overall command of Australian Major General Peter Cosgrove , INTERFET began arriving on 12 September 1999 and was tasked with restoring peace and security , protecting and supporting UNAMET , and facilitating humanitarian assistance operations . With the withdrawal of the Indonesian armed forces , police and government officials from East Timor , UNAMET re @-@ established its headquarters in Dili on 28 September . On 19 October 1999 , Indonesia formally recognised the result of the referendum and shortly thereafter a UN peacekeeping force , the United Nations Transitional Administration in East Timor ( UNTAET ) was established , becoming fully responsible for the administration of East Timor during its transition to independence . The hand @-@ over of command of military operations from INTERFET to UNTAET was completed on 28 February 2000 . Australia continued to support the UN peacekeeping operation with between 1 @,@ 500 and 2 @,@ 000 personnel , as well as landing craft and Blackhawk helicopters and remained the largest contributor of personnel to the peacekeeping mission . During these operations Australian forces regularly clashed with pro @-@ Indonesian militia and on a number of occasions Indonesian forces as well , especially along the border with West Timor . Significant actions occurred in Suai , Mota 'ain and at Aidabasalala in October 1999 . However , with the security situation stabilised the bulk of the Australian and UN forces were withdrawn by 2005 . Two Australians died from non @-@ battle related causes , while a number were wounded in action .