The huge deluge that swamped coal producing Queensland state in January caused significant damage, halting mine production and cutting key transport infrastructure, the Treasury said in its latest economic round-up.
"Contacts suggested that the loss of coal production is estimated to be between 20 million and 30 million tonnes," it said.
The government previously estimated the floods, which covered an area the size of France and Germany combined and were followed by destructive Cyclone Yasi, would cut coal production by 15 million tonnes.
Commentators said the new figure would roughly equate to a loss of between Aus$5.5 and Aus$8 billion ($8.3 billion) worth of coal production, well beyond the Treasury's earlier estimate of Aus$5 billion in 2010/11.
The report said although weather conditions had normalised, some mines were still clogged with water, adding that the economic impact of the deluge was likely to extend into the June quarter.
"Lower coal exports have been partly offset through higher prices, which have increased sharply in response to the temporary supply constraints," it said.
The report noted that while the key economic impact of the natural disasters had been on coal production and exports, there had also been significant losses in agricultural production in some states.
But while both the volume and quality of farming output had suffered, business leaders felt the rains had been good for the sector overall, it said.
"The floods and cyclone have also had an adverse effect on the tourism industry, reducing numbers during the crisis but also affecting near term prospects," it added.
Australian tourism is facing a range of problems, including ageing infrastructure, increasing competition from Asia and the high Australian dollar.
Treasury officials met with more than 50 leading businesses and organisations across the nation in February and March to produce its quarterly Economic Roundup.