Witnesses spoke of victims being shot at close range, with women and children also believed to be among those killed.
“It is clear that this can now only be described as a terrorist attack,” said Prime Minister Jacinda Ardern, saying it marked “one of New Zealand’s darkest days”.
“From what we know, it does appear to have been well planned,” she said, adding that in addition to the dead another 20 people were seriously injured.
The gunman at one mosque was an Australian-born citizen, Australian Prime Minister Scott Morrison said in Sydney, describing him as “an extremist, right-wing, violent terrorist”.
It was not immediately clear how many attackers were involved, but Ardern said three men had been taken into custody.
Two IEDS (improvised explosive devices) were also found and neutralised by the military, police said.
A Palestinian man who was in one of the mosques said he saw someone being shot in the head.
“I heard three quick shots, then after about 10 seconds it started again. It must have been an automatic – no one could pull a trigger that quick,” the man, who did not wish to be named, told AFP.
“Then people started running out. Some were covered in blood,” he said, adding that he joined the fleeing crowd and managed to escape.
Video and documents circulating online suggested the shooter had streamed his attack on Facebook Live.
Journalists experienced in verification techniques said it appeared to be genuine.
New Zealand police described it as “extremely distressing” and urged web users not to share it.
A manifesto had also been posted online on accounts linked to the same Facebook page, suggesting the attack was racially motivated.
A social media account had also posted a number of pictures of a semi-automatic weapon covered in the names of historical figures, many of whom were involved in the killing of Muslims.
Police, who initially imposed a city-wide lockdown, sent armed officers to a number of scenes.
An ashen-faced Ardern told reporters the attacks had been “an extraordinary and unprecedented act of violence”.
“It is clear that this is one of New Zealand’s darkest days,” she said.
The two known targets were the Masjid al Noor in central Christchurch, and a second mosque in suburban Linwood.
One witness told stuff.co.nz he was praying when he heard shooting – and then saw his wife lying dead on the footpath outside when he fled.
Another man said he saw children being shot.
“There were bodies all over,” he said.
An eyewitness told Radio New Zealand that he heard shots fired and four people were lying on the ground, with “blood everywhere”.
Police warned Muslims all over the country not to visit mosques “anywhere in New Zealand”. Friday is Islam’s holy day.
Christchurch city council offered a helpline for parents looking for kids attending a mass climate change rally nearby.
The Bangladesh cricket team – which had been in Christchurch for a test match against New Zealand that was later cancelled – all escaped without injury.
Mass shootings are rare in New Zealand, which tightened its gun laws to restrict access to semi-automatic rifles in 1992, two years after a man shot dead 13 people in the South Island town of Aramoana.
However, anyone over 16 can apply for a standard firearms licence after doing a safety course, which allows them to purchase and use a shotgun unsupervised.