"Sydney"s first overseas deployment as a transport was to Southeast Asia in 1964. In late May, the ship was loaded with supplies and munitions for Malaysian forces in support of the country's defence policy against Indonesia. In total, 1,245 personnel were also embarked: engineers from the 7th Field Squadron, the Royal Australian Artillery's 111th Light Anti-aircraft Battery, and four UH-1 Iroquois helicopters plus associated air- and ground crew from No. 5 Squadron RAAF. "Sydney" departed Garden Island just after midnight on 24 May. After entering New Guinea waters, the ship was put on high alert; radio and radar silence was enforced, while the anti-aircraft guns of the 111th Battery were secured to the ship's deck to supplement her armament. "Sydney" met the destroyer escorts and off the Philippines on 3 June, and a day later, the ships arrived at Kota Kinabalu, where the 7th Field Squadron was offloaded with the aid of the Australian Army landing ships "Vernon Sturdee" and "Clive Steele". "Sydney" and her companions left for Singapore at midnight on 5 June, and arrived three days later to offload 250 tonnes of ammunition. "Sydney" and "Parramatta" then proceeded to Penang, where the 111th Battery, No. 5 Squadron, defence stores, and more munitions were offloaded during 16–17 June. The return voyage to Australia was interrupted on the morning of 23 June by the detection of a suspected Indonesian submarine: the two Australian ships performed evasion tactics for eighteen hours before resuming the voyage to Fremantle. No awards were issued to "Sydney" for operating in support of Malaysia during her service life, but a reorganisation of RAN battle honours published in March 2010 saw the battle honour "Malaysia 1964" retroactively awarded to the ship.