Passengers on the Big Red Cat watched as the car barge passed a dead dwarf minke whale this week.
Crew on the barge said they believed the whale had been dead for more than 24 hours.
It had 1m gashes on its back whidch equated to being hit by a propeller at a high speed.
Onlookers said there was no indication the whale was hit by a passenger ferry despite its body being sighted in the Stradbroke ferry route area.
It was spotted in the same area the bodies of two Southern right whales were found last year.
Quandamooka man Darren Burns said the recent whale fatality highlighted the need for government agencies to focus on whales in Moreton Bay during whale season.
He said there should also be greater awareness of whales on the Stradbroke Island ferry routes.