The accused has had interim name suppression.
The man's lawyer Scott McKenna said his client had not been seen since going to get a rapid antigen test (RAT) last night but was today found at a family friend's property north of Hamilton.
Crown prosecutor Rebecca Mann said he was now heading to court in the company of police.
Judge Jonathan Down issued a warrant for the defendant's arrest at 10.30am.
This was a "particularly gruesome and troubling case, so I'm sure that he is troubled with the prospect of facing this trial", the judge said, but added the only way to deal with it was to appear before the court.
The accused unsuccessfully tried to get his charge dismissed and his trial will begin once he arrives at court.
The day of the baby's death
The court heard that just before 1pm on October 23, 2020, Bear was impounded for roaming.
The accused then turned up to the pound and provided evidence of ownership to get him released.
The next day, baby Jaxon was born at Waikato Hospital and taken to his Enderly home with his mother.
The accused and the baby's mother were in an on-and-off again relationship.
He was at the house that day and overnight and he remained there the next day but left when the mother's friends arrived.
At some point in the evening of October 25, Jaxon was placed in his bassinet and his mother went to the toilet.
She heard the baby crying out and ran to see what was wrong and found he was missing.
She ran to the rear of the property and saw Bear returning from the fence line and found the baby partially buried, with him having obvious bloodied injuries.
Two days later, on October 27, Jaxon's life support was turned off and he was pronounced dead.
'Not to rush' sentencing
McKenna was keen for his client to be sentenced this afternoon, but Judge Down said he wasn't comfortable doing that.
He said there needed to be a pre-sentence report, referral to restorative justice and consideration of emotional harm for the victim to consider.
McKenna was also keen to apply for permanent name suppression for his client especially given his mental health status.
Mann said the crown would oppose a permanent suppression application but supported further reports to be collated.
Judge Down convicted the defendant and remanded him on bail for sentencing until April.
He granted continued name suppression until that date.