Saravanaa Bhavan's Auckland website attributed the growth of the chain to founder "Rajagopal's vision and his keen desire to take his concept worldwide".
The chain - which has been described as the McDonald's of South India - has more than 80 outlets worldwide and employs close to 9000 staff.
But following the Supreme Court decision, Mani said wording on the company website would be changed and the business was distancing itself from Rajagopal.
"The brand has outgrown the creator," Mani said.
"We're revamping because this man is a hardened criminal. He may have created a great brand, but we want nothing to do with him and we are taking the brand away from the man."
Mani also apologised for the "teething problems" at the restaurants, which had seen hundreds being turned away or others not getting served last week.
He said the business had struggled to get experienced staff, partly due to New Zealand's immigration policy.
"Student workers here are allowed only 20 hours, and we can't get any permanent employees," Mani said.
"I've never seen any city in the world, including Sydney and Melbourne, where finding good employees is so challenging."
The chain has outlets in countries across the world, including Europe, North America, Middle East, South East Asia and Australia.
Businessman Vijay Arasu, 37, was one of many who walked away from the restaurant last Tuesday after he and his friends did not get their order after waiting for more than two hours.
"We are disappointed because this is a big-name restaurant chain, like the McDonald's of India, but they don't even seem to have a system," Arasu said.
On Wednesday, those who turned up at the restaurant for lunch were instead greeted with a sign which said it was closed "due to unexpected maintenance work".
Mani apologised to those who have had poor dining experience and hoped they would give the restaurant a second chance.
"To our disappointed customers, we would like them to come back and make sure they make up their minds about who we are in the next few days," Mani said.
Saravanaa Bhavan offers vegetarian dishes on its menu that are exclusive to South India and Tamil Nadu in particular, including rice idly, masala vada, mysore bonda and South Indian thali meals.
Chefs from Chennai had been brought in to train employees how to cook the dishes so it would have the same consistent taste as the chain's outlets internationally.
"The flavours will take our Indian customers back to their home villages, and an authentic South Indian experience for others who haven't been to India," Mani added.
Mani said the plan was to open several restaurants in New Zealand, with the next one most likely to be in Queenstown.
Saravanaa Bhavan is at 51E Hobson St and open daily from 11am to 10pm.