Brenton Tarrant was charged with "engaging in a terrorist act", police said in a statement on Tuesday.
He is already facing charges of murder and 40 of attempted murder following the attack on two mosques in the South Island city on 15 March.
The Australian is next due in court in June.
It is the first time a person has been charged in New Zealand with an act of terror under this law.
Police - who met with victims' families and other survivors to inform them of the charge before it was announced - said they consulted with legal experts and prosecutors before deciding to lay the additional charge.