Already facing multiple charges of murder and attempted murder, Brenton Harrison Tarrant, a 28-year-old Australian, was formally accused of terrorism on Tuesday.
Forty-two people were killed in the Al-Noor mosque and seven were killed at the Linwood mosque. Two died in hospital.
New Zealand Prime Minister Jacinda Ardern described the killings as terrorism immediately after the murders.
Police Commissioner Mike Bush said he would not comment on the charges as the case is in process, but he has informed the families of those killed and injured in the attacks that the alleged killer will be charged with terrorism.
Tarrant has already been ordered by the judge to undergo a mental health review to make sure he is fit to stand trial.
Tarrant sent Prime Minister Ardern a copy of his manifesto before he allegedly carried out the killings, spelling out his white supremacist beliefs and the violent actions he was planning to carry out on New Zealand soil.
This new charge will test New Zealand’s terrorism law which came into force in 2002 and can include life imprisonment, the maximum charge.
Tarrant is scheduled to appear in court on 14 June. The results of his mental health evaluation will determine whether he is required to file a plea at that time.