Following the outbreak of war with Japan, Collins was appointed Commodore Commanding China Force, the RN-RAN cruiser and destroyer force based in Batavia, Dutch East Indies, under the American-British-Dutch-Australian Command.
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When the war ended Collins was the RAN's representative at the surrender ceremony in Tokyo Bay.
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Relations between the RAN and British Royal Navy were close at the time, with frequent exchanges of officers between the two and in June 1941, Collins was transferred to Singapore, as Assistant Chief of Staff to the British Naval Commander in Chief, China Station, Vice Admiral Geoffrey Layton.
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In mid-1944, Commodore John Augustine Collins was made commander of the Australian-US Navy Task Force 74, and commander of the Australian Naval Squadron, with HMAS Australia as his flagship.