Remains believed to be the 54-year-old man and the girl were found after the blaze at Biggenden, southeast of Bundaberg, on December 20.
Investigators now believe the pair were killed, rather than the fire being accidentally sparked.
"A crime scene was declared and following scientific examination, investigators believe the fire to be deliberately lit," police said in a statement on Thursday.
State Emergency Service volunteers will comb a paddock near the shed for further evidence on Thursday.
Police have called for anyone for information, or CCTV or dashcam footage, to contact them.
The local bakery owner and his daughter are survived by his fiance Bec Hansen, who was reportedly due to marry Mr Mooney on Wednesday.
Callide MP Bryson Head paid tribute to Mr Mooney and Kirra three days after the fire.Â
"There is no doubt that Todd was a great man with a brilliant work ethic and a passion for baking," he wrote on Facebook.
"He supplied a number of surrounding towns with fresh pies, bread and other baked goods. This loss will be felt far and wide across the Wide Bay and Burnett."
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