The former @-@ Portuguese colony of East Timor was invaded by Indonesia in 1975 , however , following years of violent struggle the new Indonesian government of President B.J. Habibie subsequently agreed to allow the East Timorese to vote on autonomy in 1999 . The United Nations Mission in East Timor ( UNAMET ) was established to organise and conduct the vote , which was held at the end of August 1999 and resulted with 78 @.@ 5 % of voters deciding in favour of independence . However , following the announcement of the results pro @-@ Indonesian militias supported by elements of the Indonesian military , launched a campaign of violence , looting and arson and many East Timorese were killed , while perhaps more than 500 @,@ 000 were displaced . Unable to control the violence , Indonesia subsequently agreed to the deployment of a multinational peacekeeping force . Australia , which had contributed police to UNAMET , organised and led an international military coalition , known as the International Force for East Timor ( INTERFET ) , a non @-@ UN force operating in accordance with UN resolutions . The total size of the Australian force committed numbered 5 @,@ 500 personnel , and included a significant ground force , supported by air and naval forces , in the largest single deployment of Australian forces since 1945 .