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Judge Pippa Sinclair noted the objection but indicated the reasons for the video appearance were strong.
It followed last night's announcement from Chief Justice Helen Winkelmann to suspend all new jury trials for two months because of the health crisis. She said maintaining correct hygiene requirements in the court system was unrealistic.
"There is a special onus on the courts to protect the health of jurors who are performing an important civic duty."
The murder accused was granted interim name suppression and remanded in custody.
He will be back in court again in the High Court at Auckland in two weeks, where he has again requested to appear in person.
During the brief hearing, the alleged killer could also be seen on the screen making hand gestures resembling gang signs, while members of Lee's family sat in the public gallery - one holding his ashes.
A 20-year-old man jointly charged with murdering Lee also refused to appear via video link today.
He was also granted interim name suppression and remanded in custody until the High Court hearing next month, when another 20-year-old man, also granted suppression, will appear.
The fourth murder accused, a 23-year-old man, also appeared in court this afternoon via video link, was granted name suppression and remanded in custody to the April date.
All four men are also accused of attacking another man and are charged with injuring with intent to injure.
Lee was behind bars for an attack on his partner, which occurred as he held her captive at a Rotorua house for several hours.
Corrections chief custodial officer Neil Beales previously said the incident at the prison took place in a yard.
"The alleged assault occurred in the unit's yard. Staff responded to stop the assault and provide medical assistance to the victim," he said.