Tourism Whitsundays says a Federal Government decision to increase the reef tax has come at a bad time for the industry.
The levy on one day-trip ticket will increase by 50 cents to $6 from April next year.
The money raised will be used by the Great Barrier Reef Marine Park Authority to protect and manage the reef.
Tourism Whitsundays chairman Chris Jacobs says many operators will not pass on the increase to customers.
"You know our ability to increase prices further at present is not great, so it will probably be a situation where many of the operators have to absorb that increase," he said.
"Many of the big operators are carrying 100,000, 200,000 guests per year to the reef, so it's actually quite a deal of money."
Mr Jacobs says the tax increase is another blow for the industry.
"Here in the Whitsundays region, and I'm in touch with a number of operators in Cairns and up and down the coast as well, there's just no doubt that we've had sort of triple whammies of the strength of the Australian dollar, the weather events and the declining flights and visitation numbers, so it's pretty tough out there," he said.
