The men, one aged in his 30s, are in a serious condition with wounds to their legs. The age of the second victim is unknown.
They were brought by boat to the Coral Sea Marina about 11am on Tuesday (local time), where they were treated by paramedics.
"There is one patient with quite serious foot injuries," the ambulance service said.
The other has a lower leg injury.
A rescue helicopter was flying them to the Mackay Base Hospital.
The Whitsundays region has been the site of a number of shark attacks in the last year.
Victorian man Daniel Christidis (33) died in November 2018 after being attacked at Cid Harbour at Whitsunday Island during a trip with friends and colleagues.
That incident followed separate attacks within 24 hours in September - also at Cid Harbour - on Tasmanian woman Justine Barwick and Victorian 12-year-old Hannah Papps.
Earlier this year, a man was hospitalised after being bitten on the thigh in waters at Hardy Reef, about 50km northeast of Hamilton Island.
