Other charges are still under consideration.
During the half-hour hearing Justice Cameron Mander ordered Tarrant undergo two assessments to determine whether he may be mentally impaired, legally insane or fit to stand trial.
In an attack broadcast live on Facebook, a lone gunman armed with semi-automatic weapons targeted Muslims attending Friday prayers in Christchurch on March 15, killing 50 worshippers and wounding dozens of people.
Police said further charges were being considered against Tarrant - a self-avowed white supremacist - but did not specify what they were.
Although initially indicating he planned to represent himself in court, and dismissing his duty lawyer, two Auckland lawyers, Jonathan Hudson and Shane Tait, have now confirmed they will represent him, in what will be one of the most complex and lengthy court proceedings in New Zealand history. "People ask me, 'Why did you forgive someone who has killed your beloved wife?'" he said.More news: Yankees place Giancarlo Stanton on IL with biceps injury
Mr Tarrant appeared in the courtroom - packed with relatives of some of his victims - via video link from prison.
On March 16, the day after the shootings, he was charged with a single count of murder.
The court remanded Tarrant in custody until his next court appearance on June 14.
The Federal Criminal Police Office said it briefed lawmakers on its investigation into ties the alleged Christchurch mosque attacker had to Germany, including buying a ticket to Neuschwanstein Castle last November.
He's received a murder count for each of the victims who died in two mosques in Christchurch as well as 39 counts of attempted murder. However, New Zealand's complex and seldom-used anti-terrorism laws, introduced after the 9/11 attacks, could make prosecution more complicated.More news: USA attorney general defends his 4-page summary of Mueller report
She has since initiated an independent judicial probe into the twin attacks, asking the police and intelligence officials to implement a royal commission - the most powerful judicial probe available under New Zealand law.
New Zealand's Corrections Department revealed last month that Tarrant was segregated from other prisoners and able to be observed constantly, either directly by staff via CCTV camera.
"I$3 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.
Prison officials say Tarrant is under 24-hour surveillance with no access to media, according to news reports.
New Zealand is in the process of tightening its gun laws after the attack and the government has also said it will review laws dealing with hate speech.More news: 3 more accusers come forward against Biden