Provided the terms of reference were within the powers of the Commonwealth as reflected in the Australian Constitution a Commission of Inquiry is an alternative to a Royal Commission..
A Commission of Inquiry reports to both Houses of Parliament, instead of to the executive government of the day.
The executive Government has greater power to restrict the terms of reference of a Royal Commission..
More information about a Commission of Inquiry can be found on this lin where The Clerk of the Senate responds to Senator Peter Whish-Wilson:
On 2 September 2007, the then Prime Minister, John Howard, and the then Minister for Agriculture, Fisheries and Forestry announced the establishment of an inquiry into the outbreak of equine influenza in Australia in August 2007.] The Quarantine Amendment (Commission of Inquiry) Act 2007 (Cth) amended the Quarantine Act 1908 (Cth) to provide for the appointment of a person to conduct a commission of inquiry into the equine influenza outbreak and related quarantine requirements and practices.
The Commission was vested with most of the powers of a Royal Commission. In addition, people engaged to assist the Commission were entitled to exercise powers under the Quarantine Act in certain circumstances..