Strike Force Retractor was set up to investigate his disappearance.
Chris Robertson, 33, was arrested yesterday and has today faced Newcastle Local Court, charged with murder.
He did not apply for bail and it was formally refused.
Police have also searched a Rankin Park home and officers seized a number of items, which will be forensically examined.
Detectives said they would continue examining the human remains, which were found at Seahampton.
Inspector Craig Davis said the alleged murderer was known to Mr Daunt.
“The accused and Christopher Daunt were known to each other,” he said.
“They were acquaintances and friends, they had been known to each other for approximately five years.
“We’ll be alleging that the accused person assaulted Christopher Daunt, that resulted in fatal injuries,” he said
Police hope bushland find will bring closure for family
Inspector Davis said police located the remains overnight and they were kept under guard until forensic teams arrived this morning.
“We acted on some information that we received and the remains, as I understand it, were found in bushland area just off the roadway out at Seahampton,” he said.
“It’ll be alleged by the police that following the assault of Christopher Daunt, that the accused person transported the body of Christopher Daunt out to that location.”
“Chris’s family have been informed of the recent developments and of course it is tragic for those people.”
“It has been a lengthy investigation, some 13-odd months.
“If it’s any consolation, if I can put it that way to the family, at least they have some sort of closure, if the skeletal remains are confirmed to be Christopher Daunt, but of course it is a very tragic set of circumstances.”