1962 Royalist suffered permanent damage in rough weather in the Tasman Sea with the keel twisted out of alignment. The RAN captain, determined to make Auckland for a Rugby Union test between the Wallabies and All Blacks at Eden Park, had been running the ship at excess speed into a head sea. The back of the cruiser was technically broken and it could have been assessed as a 'constructive loss' and, as uneconomic to repair, scrapped. It would never be possible again for the cruiser's gun directors to determine the cruisers datum centreline necessary for accurate targeting. The cruiser operated with the British Far East Fleet, in three tours of duty in 1963, 1964 and 1965, during the Indonesia–Malaysia confrontation the crews being belatedly awarded General Service Medals for the 1963–64 tours and Operational Service Medals for active service in combat zones in 1956, 1957–1958 and 1965, finally recognised by the New Zealand government in 2000. From mid-1963, reports by the captain of Royalist noted that one of the two Mk 6/275 HALADCTs were often unserviceable, often one or two STAAGs were, while the ship's hull and lower structure was marginal requiring constant work and frequent painting, requiring an extra Asian workforce due to the construction of the cruiser out of "low quality wartime steel", and the ship's below-deck humidity and constant temperature at a minimum of . The ship's modernisation had provided only for a lifespan of six years, so these conditions were expected. Effective modernisation of the ship after acquisition from the Royal Navy only amounted to several ECM/ESM updates. By May 1964 the Indonesian Confrontation had escalated with Indonesian forces conducting cross-border raids in Kalimantan and landings in Borneo. The British Minister of Defence Peter Thorneycroft and Mountbatten requested the use of carriers and major units to conduct provocative passages, to encourage a revolt against Sukarno and his generals. After rest and recreation in Singapore, Royalist took on 580 tons of fuel oil on 14 July 1964 and the following morning took ammunition on from lighters. It left Singapore in the afternoon returning to Auckland from Singapore via the Cairns races in Queensland, transited the Carmat Straits on 15 July, Sapud on 16 July (at ABC state Yankee, at 2130 raised to condition X Ray at 2230) as it was in the Java Sea between Jakarta and southwest Kalimantan and then ran along the coast of Java