The then-28-year-old Australian murdered 51 worshippers and shot and injured 40 others.
Atacocugu wanted to retrace the path of the killer to reclaim it in peace.
He left the Octagon in Dunedin on 1 March in hopes of reaching Christchurch to commemorate the third anniversary of the shootings.
But he was admitted to hospital on Tuesday due to a blood infection.
The source of the infection remained unclear but Atacocugu had developed deep blisters on his heels during the trek from Dunedin to Makikihi.
He told RNZ this morning he would be discharged today and then continue the journey from Makikihi to Christchurch.
He said he would now bike 170 kilometres of the journey and finish it with a walk from Rolleston to Al Noor Mosque on 15 March.
"If I'm not stubborn and I don't have hope then why do the bike ride," he said, with a laugh.
"Then I'd give up and not carry on, but I want to complete this mission and I want to finish this distance against the hate.
"I never gave up my hope, I still have hope that I'll complete it and complete the mission impossible."
Atacocugu, who required many surgeries to overcome his injuries following the shootings, said he felt much better today following two days in hospital.
As part of the walk he is also raising money for the Key to Life Charitable Trust, the Child Cancer Foundation and Save the Children.
So far more than $40,000 had been donated.
- RNZ