I don't know if this question or solution has been addressed yet but I believe it is the most economical and fair.

There are 7 places on a fish that I can think of that can be used to mark a fish safely.

We have three major management programs and they are state, Native American, and wild.

Why can't the state and the Native Americans have different designated places on a fish to mark their signature?
This way it is easier to tell the difference between fish between the 3 different groups.

No nets are needed with this system because the Tribes can harvest their fish directly at their hatchery.

Sports fishermen will only harvest fish marked by the state hatchery.

And no one is allow to harvest wild stock (unmarked).

Oh, and don't forget the combinations of the 7 spots that can produce 315 different ways to mark a fish.