A charter fishing operator in far north Queensland says he is still in shock at discovering the body of a decapitated three-metre crocodile last weekend.

Gone Fishing Cairns owner Jim Millar says he found the croc beheaded on a bank at Trinity Inlet in southern Cairns while he was running a charter trip on Saturday morning.

Mr Millar says the people on board his boat were likewise in shock.

"To come to the region where everybody's coming to look at the environment whether it be the reef, the rainforest or go on a fishing trip and have a look what's going on up the inlet, and to see that happen doesn't shed a very good light on some of the locals we have here," he said.