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Indeed, ill-discipline among the Australian force appears to have been an issue—perhaps due to the haste with which the AN&MEF had been raised and the poor character of some of those that were enlisted. Claims in the Australian media of criminal behaviour caused considerable controversy at the time, and later led to a parliamentary enquiry. In the end a number of soldiers were court martialled and imprisoned for looting and theft, although more serious allegations, including rape, also arose. Following the capture of the remaining German possessions in the region, the AN&MEF provided occupation forces for the duration of the war. Holmes subsequently established a military government which continued until 1921, after which Australia received a mandate from the League of Nations to govern the territory. The Australian military administration continued the exploitative economic policies of the previous German colonial administration, and official policy was to continue the status quo, including the use of indentured Melanesian labour on plantations, the levy of the "native head tax" and official floggings, or corporal punishment. Equally, despite previously being protected by the German colonial administration in 1914, the hunting of the native bird-of-paradise, crowned pigeon and white heron for the lucrative trade in their feathers and skin, was officially condoned and a custom tax levied on their export. Under the terms of the German surrender, Haber was allowed to return to Germany, while German civilians could remain as long as they swore an oath of neutrality. Those who refused were later transported to Australia, where they could freely travel back to Germany.
On 9 January 1915, Holmes handed over command of the AN&MEF to Brigadier General Sir Samuel Pethebridge, the former Secretary of the Department of Defence. Holmes returned to Australia and re-enlisted in the AIF, as did most of his men. They were replaced by the 3rd Battalion, AN&MEF which was known as the "Tropical Force" because it had been specially enlisted for service in the tropics. Pethebridge established the administrative structures that remained through the period of military occupation. Although required by international law to follow the German forms of government, the territory gradually acquired the appearance of a British colony. As a result of the peace settlement under the Treaty of Versailles in 1919, Germany lost all of its colonial possessions, including German New Guinea. The colony became the Territory of New Guinea, a League of Nations Mandate Territory under Australian administration in 1921. It remained as such until 1949, when it was merged with the Australian territory of Papua to become the Territory of Papua and New Guinea, which eventually became modern Papua New Guinea.