Command arrangements were slightly different for the 2003 Iraq War. As in the previous deployments, the CDF, General Peter Cosgrove, was assisted by the Strategic Command Group and the staff of Strategic Command Division (later called Strategic Operations Division) under Major General Ken Gillespie. However, because of the very high level of secrecy necessary during the early phase, the initial planning was conducted by Gillespie’s staff. The COMAST, Rear Admiral Marc Bonser, was only brought into it somewhat later.

There were similarities with Operation Slipper. The Australian national commander, Brigadier Maurie McNarn, was located in Qatar, alongside the headquarters of the US Commander, General Tommy Franks. He reported to the COMAST, Rear Admiral Bonser. As in Operation Slipper, he had several task group commanders, in this case four—maritime, maritime patrol aircraft, special forces, and fighters/transport aircraft. These were placed under the operational control of coalition component commanders. They reported on operational matters to McNarn and on technical and administrative matters directly to COMAST.

The major difference between this operation and Operation Slipper, however, was that McNarn also reported directly to the Cosgrove, who believed that he needed up-to-date information so that he could report it to the government. Further, in a fast-moving operation, Cosgrove believed that he needed to be able to give orders directly to the commander in the field.

After the successful invasion of Iraq, and the end of Operation Falconer, the ADF began a new operation, Operation Catalyst. Considerable numbers of ADF units returned to Australia, but the remaining force still contained several different elements, including land and air force elements in Iraq, air force units outside Iraq, and naval units in the Persian Gulf. The command structure changed yet again. This time the ADF formed a joint task force in the Middle East, commanded by a one–star officer, initially Air Commodore Graham Bentley. While the details were extremely complex, in brief, Bentley had operational control of all the Australian components. In turn he reported directly to COMAST. As in Operation Falconer, Bentley could speak directly to Cosgrove on matters of strategic and national policy, but these occasions were fewer, and he reported more regularly to COMAST.

The conduct of the Iraq War raised further questions about the efficacy of the higher command arrangements for joint operations. In particular, there were suggestions that, as the planning for the war had been conducted by Strategic Operations Division (at least in the first instance) and as McNarn had reported directly to Cosgrove, there was no need for HQAST. Some of these criticisms were couched in terms of questioning the validity of the concept of the operational level of war, suggesting that it is no longer relevant in modern war, or at least there is no place for an operational level command structure.

This claim misunderstands the nature of the operational level. The operational level is the link between the strategic and the tactical levels, and should not merely be seen in terms of the functions of HQAST. The operational level existed before HQAST was established and does not exist in just one headquarters. The operational level planning for the commitment to the Iraq War was conducted by the Australian planning team at the Headquarters of US Central Command and also at HQAST. The operational command of the Iraq War was conducted by General Franks’ US Central Command headquarters level. Brigadier McNarn therefore worked at the operational level headquarters, even if he did not fully command at that level. The restrictions on his exercising his command were caused partly by the coalition nature of the war. When Australia provided the main deployed force, it was as in East Timor in 1999 where Headquarters INTERFET had been an operational level headquarters and the Commander INTERFET an operational level commander. Nonetheless, there were tensions between HQAST and Strategic Operations Division and there was some overlap of work. Undoubtedly, in future operations, the CDF would want to communicate directly with a deployed joint force commander, and he would need timely access to information. Further, in a small defence force it seemed wasteful to maintain a large number of headquarters.