The shark attacked a 22-year-old man who was swimming by the boat, and he suffered a calf injury.
RACQ CQ Rescue crewmen were told by the two British victims that they were "wrestling and thrashing about in the water...when the attack occurred", the rescue organization reported on Twitter.
Tracey Eastwick, manager of operations for Queensland Ambulance Service, said the shark attacked one of the backpackers before turning its attention on the other.
Emergency services were called to Hook Passage, which is a popular snorkelling spot, according to 9News.
There have been at least four shark attacks in the Whitsundays since September past year, one of them fatal.
Queensland Ambulance have said that the two men are in a "serious condition" following the incident.
A statement from Tourism Whitsundays said: "Our first thoughts are with the two people involved in the incident and their welfare; as well as the other passengers and crew on the boat".
Daniel Christidis, 33, from Victoria, was mauled to death at Cid Harbour during a boating trip with friends.
The pair was brought by boat to the Coral Sea Marina about 11am on Tuesday, where they were treated by paramedics.
Earlier this year a man was hospitalised after being bitten on the thigh in waters at Hardy Reef, about 50km northeast of Hamilton Island.
"We are going to have more and more of this happening until governments put public safety as their number one priority", state lawmaker for Whitsunday, Jason Costigan, told Australian newswire, AAP.
"We are saddened to confirm that two of our guests were injured in a shark attack this morning".
"I will not shy away from my stance that the drum lines need to go back in", she told reporters.
More than 750,000 people visit the Whitsunday Island region a year.