Investigators have remained at the Chinchilla Weir, west of Brisbane, on Tuesday after declaring the site a crime scene two days prior.
An excavator was brought in about 7am on Tuesday, with officers seen by 7NEWS at times waving for it to stop and bringing over evidence bags.
A funeral van arrived at the scene about 10.45am.
A blue tarp was used to move an object into the van before the scene was completely closed.
The remains have been taken for forensic testing, police said.
The development comes a day after Kaydence’s mother Sinitta Dawita, 28, and the woman’s fiance Tane Desatge, 40, were accused of murdering her.
The couple did not apply for bail as they faced Dalby Magistrates Court on Monday afternoon, charged with murder, torture and interfering with a corpse.
Kaydence was born in September 2014 but was last seen in 2016.
This story first appeared on 7NEWS and has been republished here with permission.