Brenton Tarrant is charged with the murder of 51 people, 40 counts of attempted murder and one terrorism charge in New Zealand's deadliest peace time mass shooting.
Appearing via video link from prison, the 29-year-old sat in silence as his lawyer read out his plea.
The 15 March attack saw a gunman opened fire on Muslims during Friday prayers.
This is the first time a terrorism charge has been brought in New Zealand.
A number of the survivors of the attack and relatives of the victims were in court for the hearing, the BBC's Sydney correspondent Hywel Griffith reported.
As lawyer Shane Tait read out his client's not guilty pleas, a number of them gasped and became tearful.
High Court Justice Cameron Mander said the trial had been set for 4 May next year, and that Tarrant would be remanded in custody until a case review hearing on 16 August.
Last week, a restriction on publishing photos of the suspect's face was lifted.