There were just over 46,000 Muslims in New Zealand during the last census in 2013, a mere one per cent of the total population.
One eye witness said that the gunman entered from the main entrance of the building and began shooting.
A series of coordinated attacks at two mosques in New Zealand has left at least 49 people dead and dozens more wounded.
In what appeared to be the worst attack against Muslims in a western country, witnesses spoke of victims being shot at close range, with women and children believed to be among those killed.
One man outside the mosque said that he prayed that the gunman would "run out of bullets".
He added: " Out of respect and in condolence for all those killed in the terrorist attack in New Zealand, I have asked for flags to be flown at half-mast".
The prime minister said the attack reflected "extremist views that have absolutely no place in New Zealand".
The attacks in Christchurch, in which 40 people were killed, were reportedly live streamed on several social media sites by the shooter and have since been used in broadcasts and shared on social media. For many this may have not been the place they were born. On Saturday, people across the country were reaching out to Muslims in their communities on social media to volunteer acts of kindness - offering rides to the grocery store or volunteering to walk with them if they felt unsafe.
In his chilling The Great Replacement' document, the assassin laid bare his deranged ideology, claiming he was influenced by far-right Norwegian mass murderer Anders Breivik, who murdered 77 people in 2011.
According to the New Zealand Herald, four people are in custody after gunmen opened fire at the mosques in the city of Christchurch. Reuters was unable to confirm the authenticity of the footage. The mosques were packed with worshippers gathered for Friday prayers. In a statement he said: "Our hearts go out to the people of New Zealand following the news of this awful act in Christchurch".
Journalist Chris Lynch, a radio host on New Zealand station ZB Radio, told CNN that one of the shootings had occurred at "the biggest mosque in all of Christchurch".
Indonesia's foreign minister Retno Marsudi said: "Indonesia strongly condemns this shooting act, especially at a place of worship while a Friday prayer was ongoing".
One man who said he was at the Al Noor mosque told media the gunman was white, blond and wearing a helmet and a bulletproof vest.
"I came to the street I saw one person got shot on his chest", he said, adding that the ambulance and police then arrived on the scene.
"They were on the bus, which was just pulling up to the mosque when the shooting begun", Mario Villavarayen, team strength and conditioning coach, told Reuters in a message.
The third cricket test was cancelled, New Zealand Cricket said later.