In a letter to the chairman of the Havasupai Tribe, Park Superintendent David Uberuaga offered to seasonally limit permits onto a piece of land that covers some 90,000 acres of remote wilderness.
Backcountry users are upset because they believe their access is being limited and the process is being carried out in private.
Federal law required the National Park Service and the tribe to negotiate access to the land, which was half of the 1975 expansion of Grand Canyon National Park.
"Right now we think that on a weekly basis, there is a handful of people back there maybe in the spring and in the fall," Uberuaga said. "It's not about denying access at all. It's about a way to get a permit."
The Park Service expects to release the first public draft of the plan this spring.
The debate has emerged as the Grand Canyon works to revise its backcountry management plan, which was last updated in 1985.
What the park is mainly looking to address are the growing throngs of people now venturing below the rim on day hikes to the river or the opposite rim, sometimes in large groups or even running full out on the trail. The Park Service considers such activities to be ill-advised.
Uberuaga expects the backcountry rules to stay the same in most areas, but he said one avenue being explored is only allowing commercial permits in some regions and canceling private trips.
It's also revisiting rules for usage in areas like Great Thumb, Pasture Wash and Deer Creek, which was also recently "temporarily" closed down to canyoneering because some tribes see the area as the sacred place they go after death.
Uberuaga says that for decades people have been trespassing on tribal land to reach Great Thumb because the Havasupai Tribe refuses to grant permits.
But canyoneers believe the superintendent is not aware just how many people will be left out by the deal.
Many backcountry users sneak into Great Thumb or drive to the North Rim and trek with all their gear, then use small pack rafts to make it across the Colorado River.