In late May 2000, Waller became the first Australian submarine to operate as a fully integrated component of a United States Navy carrier battle group during wargames. Waller’s role was to search for and engage opposing submarines hunting the aircraft carrier USS Abraham Lincoln, a role in which she performed better than expected. A few days later, as part of the RIMPAC 2000 exercise, Waller was assigned to act as an 'enemy' submarine, and was reported to have successfully engaged two USN nuclear submarines before coming into attacking range of Abraham Lincoln. Waller performed similarly during the Operation Tandem Thrust wargames in 2001, when she 'sank' two USN amphibious assault ships in waters just over 70 metres (230 ft) deep; although the submarine was 'destroyed' herself later in the exercise.
During a multinational exercise in September 2003, which was attended by Waller and sister boat Rankin, Waller successfully "sank" a Los Angeles class nuclear submarine, prompting claims from the USN that diesel submarines like the Collins class are one of the major threats facing modern navies.