Cohen said the changes aim to help the native fish recover.
"Our native fish are amazing, but they are in real trouble. They need healthy habitats to live in and they need a fishery that gives them a chance to recover."
Four of the fish species that make up whitebait - juvenile native freshwater fish - are threatened or in decline.
There are currently very few restrictions around the whitebait season, run from August 15 to November 30.
Following a DoC consultation on whitebait management, Cohen said fishers and non-fishers show support for stricter rules around managing and monitoring the whitebait fishery.
However, Hunting & Fishing Guns and Tackle Napier salesman, and keen whitebaiter, Kelvin Hampton disagreed with the introduction of a licence.
"You don't need a licence to go and catch snapper in the ocean, but there obviously should be a catch limit otherwise it can get ridiculous."
Hampton said prior to this whitebait season, he noticed large quantities of juvenile fish when fly fishing in the Ngaruroro and Esk rivers.
"It's a really tough one to argue with. Out of season, I've seen so much whitebait going up the rivers early," he said.
DoC freshwater manager Elizabeth Heeg said the conservation minister has been fully briefed on the recent consultation and DoC's engagement with New Zealanders to improve whitebait management.
The minister is expected to make a decision about new whitebait fishing rules before the next season.
Other options consulted on by DoC include phasing out exports, shortening the season and creating some river "refuges" for whitebait.
Cohen said Fish & Bird want to act now to ensure fish populations are thriving in the future with rules that support long-term freshwater ecosystem improvements.
"Ultimately, if there are plentiful fish there can be plentiful fishing without worry. But we need to see the adult fish upstream returning to abundance before that's possible."