Beekeepers have reported dozens of stolen hives, containing nearly 500,000 bees in total.
The thefts took place across two sites on the Atherton Tablelands.
Police are investigating the incident and suspect the culprit is a semi-commercial to commercial beekeeper.
Police are investigating the thefts of multiple beehives worth tens of thousands of dollars from properties in Far North Queensland.
Investigators say they believe frames of bees and their broods were taken from 41 commercial hives on the Atherton Tablelands, west of Cairns, and put into the thief's separate hive boxes.
Commercial beekeeper Jack Laughton was "distraught" when he first discovered 14 empty beehives at a property in Kairi on September 10.
"It's a bit of a shock to the system just to open a [hive] where you would normally see bees, expect a full, healthy hive, and there's just nothing."
Mr Laughton said each hive contained about 15,000 bees, nearly 500,000 stolen in total.
Tom Bidner, who managed Mr Laughton's beehives, said over the next two days, another 27 hives were found empty at a Mutchilba property.
"Beyond that, we've lost anywhere up to $10,000 worth of pollination income.
"Then we are setting ourselves up for our main honey season, so there'll be the flow-on of that over the next three to four months of our best … honey-production time."
Mr Bidner said the entire breeding system of each hive, including the queen, had been taken.
Varroa mite was detected in Far North Queensland last week, and he said this issue, on top of the pest threat, was adding further stress.
"It's just a double whammy for us at the moment," he said.
Mr Laughton and Mr Bidner have reported the thefts to the police.
Detective Sergeant Ben Cross from the Mareeba Rural and Stock Crime Squad said he suspected the perpetrator was an experienced beekeeper.
"From what we can understand, from where they've been taken and what the purpose of the bees was and their location, we're of the belief that it's possibly more of a commercial operation than a hobby farmer."
He said beehive thefts were not common but had occurred before.
He urged anyone with information to contact Crime Stoppers.
Mr Bidner said he believed those responsible knew what they were doing and how to handle bees.
"This doesn't take 10 minutes. This is someone [who has] been there for a couple of hours and likely more than one person helping achieve this in that sort of time frame," he said
"[The hives] are most likely sitting on someone's farm right now doing pollination with them totally unbeknownst."
Sergeant Cross said that while these thefts affected the beekeepers involved, they also hit farmers who rely on pollination for crops, in horticulture.
"These commercial operators have their hives on farms for the purpose of pollination to increase crop and also fruit yield, and that impacts [farmers]," he said.
"When those colonies are diminished, it's going to be a knock-on effect there.
"The beekeeper doesn't get their money from the farmers for having the hives there; the yield is decreased also in terms of honey from those hives, and then also from the fruit that then is not produced on those farms."