The agency said there is no indication the hunter was involved with illegal marijuana cultivation, which a local fire chief had speculated as the possible cause of blaze.
No arrests have been made, and the hunter's name was being withheld pending further investigation, according to the Forest Service.
The Rim Fire began on Aug. 17 in an isolated area of the Stanislaus National Forest and has burned nearly 371 square miles - one of the largest wildfires in California history.
Officials said 111 structures, including 11 homes, have been destroyed. Thousands of firefighters were called in to battle the blaze, which at one point threatened more than 4,000 structures.
The blaze is now 80 percent contained.
Chief Todd McNeal of the Twain Harte Fire Department told a community group recently that there was no lightning in the area, so the fire must have been caused by humans. He said he suspected it might have caused by an illicit marijuana growing operation.
But the U.S Forest Service said on Thursday no marijuana cultivation sites were located near the origin of the fire.