Maj Gen Ellwood will fill a vacancy left by Brendan Moon, who was appointed as the first coordinator-general of the National Emergency Management Agency in September.
The veteran of Kosovo, Timor Leste, Iraq and Afghanistan has been co-ordinating efforts to clean up and rebuild after floods killed 13 people and damaged more than 9000 homes and businesses in early 2022.
He's also previously co-ordinated the Australian Defence Force's response to the Black Summer bushfires in 2019-20.
Premier Annastacia Palaszczuk has welcomed Maj Gen Ellwood's appointment as the reconstruction authority's chief executive officer by a selection panel.
"Major General Ellwood was responsible for co-ordinating one of the biggest recovery operations our state has ever seen following last year's flooding event," she said in a statement on Friday.
"I was aware of Jake's significant achievements when I appointed him as recovery co-ordinator and I welcome his appointment as CEO of the leading reconstruction authority in Australia."
The authority was set up after the devastating 2010-11 season of Queensland floods and Tropical Cyclone Yasi, before being made a permanent agency in 2015.
It has responded to 103 natural disasters since its formation, and was the first state disaster recovery agency to be established.
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