One of Brisbane's iconic tourist boats has crashed into an unknown object while carrying about 50 passengers, causing one person to fall through a floor and onto the lap of another passenger on the toilet below.

The impact smashed a hole into the upper deck of the Kookaburra Queen II, tearing a railing off.

A passenger said they heard a bang as another passenger fell through to the lower deck.

Ambulance crews treated people for minor injuries at Eagle Street Pier, where the ship docked, with three taken to hospital.

Queensland Ambulance Service spokesman Warren Painting said it was not known what the paddlewheeler hit this afternoon, but two people in their 70s and a woman in her 30s suffered minor injuries.

He said they were taken to the Royal Brisbane Hospital as a precaution.

Police are investigating what caused the paddlewheel boat to crash. ( ABC News: George Roberts )

"The commercial vessel was on the Brisbane River, struck an unknown object and the resulting jolt caused the injury of three passengers on board the vessel," he said.

"The Bicycle Response Team was the first unit on scene and then there was also two other transport units and a supervisor.

"Conditions were pretty smooth today — it seemed to be a nice sunny day."