It has been revealed in court that police searching for the remains of Daniel Morcombe found more clothing and bone fragments than first disclosed at a rugged Sunshine Coast hinterland site.

Brett Peter Cowan faced the first day of a committal hearing in the Brisbane Magistrates Court charged with the 13-year-old's murder and a string of other charges including indecent treatment of a child.

It has been almost nine years since Daniel went missing on his way to buy Christmas presents for his family on Queensland's Sunshine Coast.

The court yesterday heard Cowan allegedly abducted Daniel then took him south to the Glasshouse Mountains where he unlawfully and indecently dealt with him, then murdered him.

Timeline: Daniel Morcombe Look back at key developments in the case

Cowan is also charged with interfering with human remains nearly three weeks later, on Christmas Day.

The court heard evidence from police who coordinated the two-month search for Daniel's remains in the steep, swampy site near the Glasshouse Mountains last year.

Until the hearing, police had only confirmed human bones and shoes had been found, but it has been revealed a dive squad also found a pair of underpants, surf shorts, a belt and some other fabric buried at the bottom of a creek on the site.

The man in charge of the forensic examination of the site, Police Inspector Arthur Van Panhuis, told the court the clothing was found in a different area to the human remains.

He said search crews found the bone fragments by crawling on their hands and knees, shoulder to shoulder, and digging between five and 30 centimetres into the dirt and mud.

Inspector Van Panhuis told the court it was a painstaking process.

"The remains that we were finding were exceptionally fragile," he said.

"If we'd used mechanical means they might have been damaged further."

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Inspector Van Panhuis said police had information that Daniel's remains would be near a small pond towards the bottom of the search site, but most of the remains were found about 40 metres north of there.

Cowan's lawyer, Michael Bosscher, told the court it did not seem any of the remains were near the site the police had indicated.

He said the remains "seem to be following the progression north, going away from the primary search site".

"It's another item that moves away from an explanation that the bones could have been removed naturally from that site."

Inspector Van Panhuis told the court police called in a number of scientists during the search.

He said they established the remains were not brought in by animals or deposited north then washed south, and the external body decomposition was not caused by water.

Allowed to attend

Sorry, this video has expired Morcombes attend murder committal hearing

Daniel's parents, Bruce and Denise Morcombe, sat quietly in the court listening to the five charges their son's alleged killer is facing.

Mr Morcombe says some of the evidence from search site is disturbing.

"Clearly some of those photos capture images that are disturbing to family members and are difficult for us to cope with," he said.

"But certainly the terrain shots - we've been out there a couple of times to pay our respects to Daniel, and so there was nothing new there.

"But I think everyone can appreciate the rugged terrain. It is certainly not a sports field."

There were concerns the Morcombes may not be able to hear the evidence as they are both expected to be called as witnesses, but the magistrate has allowed it.

"Obviously the family is very pleased we're able to stay and listen to the evidence first hand, and of course we thank the judge for his decision on that," Mr Morcombe said.

The committal hearing is expected to run for two weeks before Christmas and resume next year.