This was the command structure in place during the Persian Gulf crisis in 1990 and the subsequent war to eject Iraq from Kuwait in the early months of 1991. Gration exercised command at the strategic level with the advice of the augmented COSC. This consisted of the Service chiefs, the VCDF (a position that had been established a few years earlier), the Secretary, and other key civilian and military staff. He was assisted by the HQADF operations staff, headed by the Assistant CDF (Operations) (ACOPS), Rear Admiral Rod Taylor. The Maritime Commander, Rear Admiral Ken Doolan, was responsible for deploying the two RAN task groups to the Persian Gulf. The task groups were commanded at sea by the Commodore Flotillas (COMFLOT), while Doolan remained in overall command of Operation Damask.

The Gulf commitment appeared to justify the broad ADF command arrangements that had been introduced during the previous five years. HQADF developed the strategic mission and passed it directly to Maritime Headquarters for its implementation. In view of the speed with which events moved, and their possible sensitivity, this was a much more efficient arrangement than the old system, which would have interposed Navy Office in the chain of command. Navy Office was kept informed throughout. The ability of Maritime Headquarters to command the task group in the Gulf was enhanced by its occupation of its new headquarters building just prior to the deployment, and by the development of the Maritime Intelligence Centre.

The Persian Gulf commitment caused no major change to the command structure, but it signalled an increase in ADF deployments abroad, most of which were mounted and commanded by one of the joint commands. Both the commitments of a signals regiment to Cambodia in 1992–93 and of an infantry battalion group to Somalia in December 1992–May 1993 were mounted and commanded by Land Headquarters. Joint exercises in Australia pointed to the necessity for a commander who could coordinate the operations of the joint environmental commanders. In 1993, Lieutenant General John Sanderson, who had commanded the United Nations force in Cambodia, was appointed CJFA and he did considerable work on the responsibilities and scope of an operational level commander in an Australian setting. But, as CJFA, Sanderson had no command responsibilities.