The discovery comes just weeks after a headless croc body was discovered on the banks of Lake Moondarra near Mt Isa.
The latest, a four-metre headless carcass, has been found at the Herbert River near Townsville.
Crocodiles are a protected species under the Nature Conservation Act.
Det Sen Sgt David Barron says police are working with wildlife officers to investigate circumstances around the unlawful killing of the freshwater crocodile.
“It is of concern to all that someone is prepared to slaughter animals in this area. Forensic evidence has been recovered from the scene and inquiries are ongoing.”
“Multiple offences have been committed in this instance against that legislation – freshwater crocodiles do not pose any threat to people who use the lake.”