New Zealand Police Commissioner Mike Bush confirmed two of those in custody were arrested at the scene, and that police were working to establish whether they had had any involvement in the incident.
Brenton Tarrant, in white prison suit, barefooted, handcuffed and flanked by two armed police officers, made a brief appearance in the court for about five minutes.
Police say they will continue guarding mosques around the country until further notice.
Whether it was at her media conference in the immediate aftermath of the Christchurch mosque massacre on Friday or comforting the devastated Muslim community in the shaken city yesterday, the 38-year-old leader has displayed the right balance of strength and compassion in the aftermath of the atrocity that killed 49 and injured 39 more.
In the video live-streamed by Tarrant, a man inside a mosque appears to say: "Welcome brother", as a gunman approaches. Worshippers, possibly dead or wounded, lay on the floor, the video showed.
People have also been laying flowers outside of mosques in other parts of New Zealand in solidarity with the victims and their famlies.
While the main court proceedings will take place in New Zealand, there will be an investigation into Tarrant's background in Australia, according to Prime Minister Morrison.
Police said the suspect took seven minutes to travel to the second mosque in the suburb of Linwood, where seven people were killed. No images have emerged from there.
The Christchurch attacker could have killed even more people as he was on the move at the time of his arrest, and had more firearms in his vehicle, New Zealand's PM said, praising police who responded to the call in just 36 minutes.
A spokesman from Ardern's office confirmed the document was sent to a generic address not checked by the prime minister herself, as part of a bulk email that also went a number of senior New Zealand political figures and large number of domestic and worldwide media organisations.
The President of French Polynesia, Edouard Fritch sent a message of support to New Zealand Prime Minister Jacinda Ardern, following the attack in Christchurch. If the would-be attacker has criminal or terror-based intentions but lacks any criminal or terror-based history, gun control will never stop him.
After the suspect left the court, the judge said that while "there is one charge of murder brought at the moment, it is reasonable to assume that there will be others".
Khokhur, 58, and husband Mehaboobbhai Khokhur, 65, had travelled from India to spend time with their son Imran, their first visit in the eight years since he moved to New Zealand. He said he survived by playing dead, but was desperate to know what happened to his friends who were there with him.
On Saturday, Christchurch Hospital said 39 people remained in hospital, 11 of them in intensive care.
People gather at a vigil for Christchurch shootings victims at Lakemba Mosque in Sydney, Australia, March 15, 2019 in this picture obtained from social media.