The death raises the toll from the attacks on 15 March to 51.
Turkey's Foreign Minister Mevlut Cavusoglu said on Twitter the man who was "critically wounded in the treacherous attack in Christchurch" had died.
Police said in a statement they were informed late last night that a man injured in the Al Noor Mosque on 15 March had died.
The 46-year-old had been in a critical condition in Christchurch Hospital since the terror attack.
The man's brother told Turkey's state-run Anadolu news agency that his injured relative was taken to surgery on Thursday, but could not be saved.
"He had surgery today, they couldn't stop the bleeding so we lost him. We were happy because we thought it was going well, he had been battling for 50 days," his brother said, according to Anadolu.
Prime Minister Jacinda Ardern said in a statement the sad news would be felt across Turkey as well as New Zealand.
"This man has been in intensive care since the attack. We have all been hoping for the best however he has now succumbed to the injuries sustained in the shooting at the Al Noor Mosque.
Ms Ardern thanked the medical staff who had been caring for those injured in the attacks.
"I want to acknowledge all the medical staff who have cared for the 49 men, women and children who were shot and wounded in the attack and taken to hospital.
"This is only the second victim to die while in hospital - the first was unable to be resuscitated on arrival on the 15th of March. This a testament to the extraordinary work put in by the medical staff at Christchurch, Burwood and Starship Hospitals in the aftermath of the shooting to save lives."
Muslim community advocate Guled Mire said many in the community had been keeping the injured man very much in their prayers.
"The community will always come together and rally behind the family and support them in whatever way is possible.
"We'll very much be keeping him in our prayers throughout the course of Ramadan, as well as everybody else we've lost in this tragic event, but also those in hospital recovering."
Nine people shot in the attacks remain in hospital and are all in a stable condition. Three Turkish citizens were among the wounded, AP reports.
Christchurch mayor Lianne Dalziel said it was extremely said news and offered condolences to the family as well as acknowledging hospital staff who had worked so hard to save the man's life.
Ms Dalziel said many families were still struggling in the aftermath of the terror attacks.
"We have focused on the number of people who have died but there were very serious injuries inflicted in that terror attack on that day and a lot of the families are still struggling with the impact of that."