Ngai Tahu is charging a levy on commercial fishers working at Lake Ellesmere in Canterbury.
Te Rununga o Ngai Tahu chair Mark Solomon says the permit system for commercial users has been introduced as way of ensuring Lake Ellesmere is maintained.
The new system means local fishers will lose 8% of their yearly takings.
The iwi, which owns the lakebed, has been working with the Department of Conservation since 2005 on a plan to restore the lake as a tribal food resource and to restore the lake environment for the use and enjoyment of all New Zealanders.
Mr Solomon says all proceeds gained through the permits will go directly towards planting, lake monitoring, research projects and enhancement of the fishery.
He says people who use the lake for recreational purposes will not be affected.
Green Party conservation and fisheries spokesperson Meteria Turei says it is only right the fishers contribute to maintaining the lake, as their industry depends on it.
The fishers say they are happy to pay but that Ngai Tahu failed to properly consult them before implementing the scheme.