"Every farmer in the region that's been affected has been impacted," Jo Sheppard from Queensland Farmers’ Federation said.
Ms Sheppard said with supply routes cut, some dairy farmers were forced to dump milk, while fruit growers impacted by transport delays have also struggled to get their produce to market.
Federal Agriculture and Emergency Management Minister Murray Watt said the clean up was well under way but the damage was significant.
"This is going to be a long recovery effort, this has been a major national event," Senator Watt said while visiting Cairns before Christmas.
Mango farmers who were already struggling to produce a good crop in Queensland's north are now facing extensive damage.
Joe Moro says his mango farm near Mareeba copped a deluge of 1.2 metres of rain over five days, ruining about half his crop and costing him half-a-million dollars.
His 14 workers resumed harvesting on December 21 after a two-week delay.
"Half my crop has either been damaged by the flooding, totally black, can't be harvested at all, or it's ripening and dropping onto the ground," he said from his farm west of Cairns.
Mr Moro is also the president of Queensland Fruit & Vegetable Growers, and said the damage to agriculture across the region was severe.
"Every crop has been affected in some way," he said.
"Papaya trees are falling down, heavily blemished fruit, banana trees are falling down and sometimes some of that crop is also in water.
"Even the avocado crop, which hasn't been harvested yet, there would be some impact on those growers as well."
Nursery owner Elaine Duncan is also counting the cost of the damage and will be continuing to clean up over the next week.
"The worst of it was the torrential rainfall and coming to work and seeing a nursery full of rotting plants," she said.
“It was probably around $300,000 to $500,000 worth of damage and loss of crop and ongoing trade."
The nursery is a major grower of seedlings for far north Queensland, supplying home gardeners and hydroponic farmers with everything from tomatoes to basil and capsicums.
The damage is still being assessed across the region, and Queensland Farmers’ Federation said it was likely to be several weeks before the full extent is known.
Disaster assistance loans of up to $250,000 are available to primary producers impacted by the cyclone.
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