IN Daniel Morcombe's final moments, he knew he was about to be molested and died trying to escape the clutches of his attacker.

Brett Peter Cowan, in secret recordings, allegedly told undercover police officers he broke the teen's neck accidentally before he could interfere sexually with the Sunshine Coast 13-year-old.

"I never got to molest him or anything like that," he allegedly said.

"He panicked and I panicked, I grabbed him around the throat and before I knew it he was dead."

Cowan, 42, allegedly confessed he had offered Daniel a glass of water to lure him into a demountable house off Roys Rd at Beerwah.

Cowan allegedly said he pulled Daniel's pants down but thought Daniel was going to run so he "choked him out".

"I had hold of his pants," he allegedly said.

"When he went 'oh no' and pulled his pants back up and tried to get away, we both went to ground and pulled me arm in tight and heard a 'ch'."

Crown prosecutor Glen Cash told Brisbane Magistrates Court Cowan thought that sound was a bone snapping.

Mr Cash did not detail what happened next but said Cowan allegedly put Daniel's body in the back of his car and drove towards bushland at the end of Kings Rd at Glasshouse Mountains.

"He describes taking Daniel's body out of the car, dragging him down an embankment and ultimately leaving the body near a tree near some water," Mr Cash said.

"(Cowan) describes to the undercover police officer he had, at the scene where he left the body, removed Daniel's clothes, made some effort to cover the body with branches and leaves, and thrown the clothes into a creek which was a little bit away from where the body was left."

Detective Senior Sergeant Stephen Blanchfield told the court the place Cowan had shown undercover police was where they found Daniel's remains, identified through DNA evidence.

The court heard Cowan told the officers he returned to the site seven to 10 days later with a shovel to bury Daniel but found only a small bone left.

Daniel's father Bruce, outside court, said that listening to Cowan's alleged confession about how his son died was "grim".

"We took it on the chin but it's very difficult to listen to and remain composed," he said.

"For over nine years we've wondered what happened and now there's certain suggestions."

Mr Cash - in recounting parts of the secret recordings made on August 9 and 10, 2011 - said Cowan allegedly said he saw Daniel waiting for a bus on Nambour Connection Rd at Woombye on December 7, 2003.

Mr Cash said Cowan told officers he turned around, parked at a nearby church carpark and made his way through "shrubbery" to approach Daniel.

The court heard he did not speak to Daniel initially, just pretending he was waiting for the bus, too.

"Observing a bus drive past he offered Daniel a lift, suggesting that he too was going down to the shopping centre at Maroochydore," Mr Cash said.

"He describes Daniel accepting the offer of a lift"

"Rather than take Daniel to the shopping centre he drove to a demountable house … saying to Daniel he has to tell his wife where he's going and offering to give Daniel a glass of water".

Cowan's lawyer Michael Bosscher asked Snr Sgt Blanchfield whether this alleged confession meant conflicting witness versions of what happened while Daniel was waiting for a bus could be discarded.

"We would, if those admissions are true, have to discard as being factual all those witnesses who describe a child hitting and fighting?" he questioned.

Mr Cash labelled the question unfair, arguing Mr Bosscher was suggesting there were only two possibilities.

"That is the confession is incorrect and those witnesses are right or the reverse," he said.

"Or there is a third possibility that is ignored in the question.

"It completely ignores the possibility that those witnesses saw a blue car, saw the things they described but what they saw was not Daniel Morcombe being abducted."

The committal hearing continues on Thursday.