Problems during the handover process and the need to repair previously unidentified defects meant the ships did not enter operational service until the end of the decade.

In the early 1990s, the RAN initiated a procurement project to replace HMAS Jervis Bay with a dedicated training and helicopter support ship.

At around the same time, the United States Navy (USN) began plans to decommission fifteen of their twenty Newport-class tank landing ships, offering them for purchase by various countries.

[5] This last-minute move was part of a sale blockage for the fifteen surplus Newports to nine nations, and was caused by the United States Senate Committee on Armed Services in an attempt to pressure US President Bill Clinton on the perceived running-down of the USN's amphibious warfare capability, as well as the concerns of one Senator over human rights in Morocco (one of the other nations slated to acquire a ship).

[7][8] After transferring into the RAN and arriving in Australia, Kanimbla and Manoora spent two years docked at Fleet Base East before they were moved to Forgacs Dockyard at Newcastle, New South Wales in June 1996, where they underwent conversion from tank landing ships to amphibious warfare transports.

[14][16] These included large quantities of corrosion, faults with the deck crane and alarm system, the need to overhaul propulsion machinery, power generators, and air conditioning, and an outdated communication suite.

[16] On 1 November it was reported that the two vessels might never put to sea again due to their poor condition,[17] but a Navy spokesman was quoted the next day as saying that they would both be repaired by early 2011.

[20] At the time of the February 2010 announcement, the intention was to repair Kanimbla return her to active service by mid-2012, and let her continue operating until her original 2014 decommissioning date.

[19] However, the predicted time frame and cost of the repairs (18 months and over $35 million), and the successful acquisition of the British landing ship dock RFA Largs Bay (which entered RAN service at the end of 2011 as HMAS Choules) prompted the Australian government to announce plans on 18 August 2011 to decommission Kanimbla at earliest opportunity.

[26] However, the government chose not to go ahead with this, as it would cost $4 million each to prepare them for scuttling, and could provoke similar reactions to the contested sinking of the frigate HMAS Adelaide.

[27] Because the two vessels were originally owned by the United States of America and were sold to Australia, their disposal had to receive US government approval and comply with International Traffic in Arms Regulations.