The Office of the Clerk operates under a dedicated Act of Parliament (Clerk of the House of Representatives Act 1988) and is part of the legislative rather than the executive branch of government. It is a non-public service department and is separate from other agencies in the parliamentary complex including the Parliamentary Service.
The Clerk of the House is appointed by warrant by the Governor-General. The Speaker recommends the appointment after consulting with the Prime Minister, the Leader of the Opposition, and other members.
For further information see Clerk of the House of Representatives Act 1988