Queensland police have shot a man dead after a 12-hour stand-off near Cairns.

Chief Superintendent Brian Huxley said the man was shot in waist-deep water at Thomatis Creek, off the Captain Cook Highway, after he allegedly raised a gun towards police.

He said the man was critically injured when police returned fire and was pronounced dead at the scene.

Earlier on Sunday, police were called to a break-in at a telecommunications building off the Captain Cook Highway.

A man then allegedly fired shots at police and rammed multiple police vehicles with his car, which later caught fire and exploded.

Police confirmed an officer was injured.

An hour later, the man fired shots at a helicopter and police who were trying to locate him.

About 3:15pm, he was found in waist-deep in water in Tomatis Creek.

The man allegedly rammed multiple police vehicles with his car. ( ABC News: Marian Faa )

Superintendent Huxley said a special emergency response team in a boat reached the man.

"As a result of attempts to apprehend him, they have been threatened and they have returned fire," he said.

The man was critically injured and pronounced dead at the scene.

"Every attempt to try and save this man's life has failed," he said.

"This is a tragic set of circumstances."

His death is under investigation by the Ethical Standards Command on behalf of the state coroner.