She denied Pakenham bail and suppressed the legal arguments from his lawyer and the police.
Pakenham is due to reappear in the Thames District Court next month.
His lawyer, Ian Tucker, said an application for electronic bail would be made then.
Ms Niethe's former husband, Terry Niethe, was watching from the public gallery and said he clapped as Pakenham was remanded in custody. "I am very pleased."
He said the decision brought some relief for Ms Niethe's mother and children.
"It's the kids that feel it the most ... and her mum."
He said the family were happy that police had made an arrest and he planned to be at every one of Pakenham's court appearances.
Mr Niethe described his former wife as a "good lady" and a great mother who loved her children.
Ms Niethe's friend Rachel Mains also spoke of a mother dedicated to her children.
"She would walk over hot coals for her babies."
Ms Mains said Ms Niethe was always there for her and cut the umbilical cord of her first child.
She said the news of the arrest had left her "a bit lost ... a bit numb".
"We all want her home, we want to lay her to rest, that's her mum's main wish. We want to find out where she is; that's what we all want."
Ms Niethe was reported missing in March 2003 when she failed to come home after visiting a man.
The last confirmed sighting of her was on closed circuit television in Ngatea, where she stopped to make a purchase on her way home.
Police spent months searching for Ms Niethe but even a $50,000 reward failed to generate any real leads.
A full review of the case was launched last November.
