The 28-year-old Australian national appeared via audio visual link from custody in the High Court at Christchurch this morning.
Around 50 family members of the mosque attack victims filed into the courtroom to watch the proceedings.
Justice Cameron Mander ordered two health assessors' reports, which defence lawyer Shane Tait said could take two to three months to complete.
The judge stressed that the move was "normal procedure" and an "entirely ordinary and regular step" to be taken at this stage of the judicial process.
Nothing should be read into the ordering of the reports, he added.
The Crown also sought an interim suppression order for the victims relating to the 39 attempted murder charges.
Justice Mander granted the order – which was not opposed by the accused's new defence lawyers Shane Tait and Jonathan Hudson – on the grounds of undue hardship.
Charge documents lodged with the court today only refer to the 39 attempted murder victims by alphabetical-numerical numbers, starting with 'W001' and ending with 'W039'.
The accused was remanded in custody to reappear in court on June 14.
Accused gunman a 'coward': victim's son
Outside court, Yama Nabi whose father was Haji Daoud Nabi was killed at Al Noor Mosque said it was important he was at court today.
He described the alleged gunman as a "coward".
Nabi said it would be a long process but he wanted justice.
Other victims' families declined to comment as they left the courthouse, saying they had been advised to not speak about the case to media.
Nabi had attempted to attend the accused's first court appearance but was prevented from entering the courtroom.
"[I] just want to see what he has to say, what sort of feeling he's got [his] emotion, to see what his reaction is, good or bad and the truth will come out of him," Yama Nabi told RNZ before this morning's court hearing.
"They didn't harm him, no one harmed him."
Farid Ahmed, who lost his wife in the attack, has famously already forgiven the alleged mass murderer.
"I have forgiven him and I am sure if my wife was alive she would have done the same thing," he previously told the Herald.
"I hold no grudge."
But Nabi told RNZ he was not willing to do that at this stage.
"How can you forgive someone if your father's not calling you, talking to you on the phone, putting a smile on your face from morning to night?
"How can you forgive someone for doing that? I mean in the end it's in the hands of Allah almighty god."
