Likewise, corporate governance experts say, the insider culture at Komen’s headquarters, with national executives and board members deeply loyal to Ms. Brinker, discouraged independent efforts.

“They are too insular,” said Daniel Borochoff, the president of CharityWatch, a watchdog group that rates nonprofit organizations.

Through Ms. Aun, Ms. Brinker declined to be interviewed.

The heart of Komen’s fund-raising effort is its grass-roots network of 122 United States affiliates, which collectively stage 135 races annually. Now, affiliate leaders say, they are trying to restore the group’s reputation in their own communities by explaining how they finance local programs to serve local health needs. It is a strategy that distinguishes affiliate activity from the actions of the national group.

Under Komen’s franchise-like model, affiliates operate as independently incorporated nonprofits but must abide by the national group’s policies. Affiliates can spend up to 75 percent of their net income on local programs — like breast cancer screening — of their own choosing. The other 25 percent goes to the national Komen organization, where it is used to finance scientific research grants.

Some affiliates publicly objected in early February after the national headquarters tried to implement a new policy that would have prohibited the local chapters from financing programs by organizations under government investigation. The policy change threatened 19 Planned Parenthood programs that had received grants from Komen affiliates. Although Planned Parenthood was not the subject of an official investigation at the time, a Republican congressman, Cliff Stearns of Florida, was looking into whether the group had spent public money on abortions.

Having failed to anticipate a backlash among affiliates and the public, Komen headquarters compounded the problem, local officials said, by acting too slowly to apologize and reverse course.