Mark King Jeffrey, 22, charged with first-degree murder, will be back in court June 3.
Out of concerns for Jeffrey's safety at the Baffin Correctional Centre (BCC), Jeffrey is being sent to an undisclosed facility outside of Nunavut.
"I'm not saying which facility he was moved to for his own safety," said Ron McCormick, Nunavut's director of corrections.
McCormick said because the case is high profile, extra precautions have to be taken.
"This was a brutal crime and so the guy has to be isolated," he said. "When a guy has to be isolated in a small facility like BCC, it's not very good. There's not very much space and there are very few opportunities for him to exercise. We have to look after him."
The date for Jeffrey's next appearance was set April 8 after defence lawyer Sue Cooper appeared in the Nunavut Court of Justice on her client's behalf.
Jeffrey was brought to the courthouse from the Baffin Correctional Centre but did not appear in court.
At last week's court appearance, friends and family of 13-year-old Naglingniq lined the hallway and filled the seats in the courthouse.
The RCMP investigation into Naglingniq's death has been ongoing since her body was found in her home on Dec. 6.
Police arrested Jeffrey on March 24 and laid charges the following day. He has been in custody ever since.
RCMP said the arrest was made after many hours of investigation and with the cooperation of residents of Iqaluit as well as a U.S. based police agency.
Jeffrey is the second person to be charged for the 13-year-old girl's murder. Charges against another man were stayed after evidence was found insufficient.
He'll be back in court on June 3 in Iqaluit.