In a statement, the Susan G. Komen for the Cure said it had accepted the resignation of Karen Handel, its senior vice president for policy since April 2011 and a one-time Republican candidate for governor of Georgia.
"I have known Karen for many years, and we both share a common commitment to our organization's lifelong mission, which must always remain our sole focus," Komen founder Nancy Brinker said. "I wish her the best in future endeavors."
On Friday, Komen reversed its decision to stop funding breast screenings at Planned Parenthood clinics after an outcry over the move triggered a political and fund-raising backlash by women's health advocates.
Handel, 49, was widely believed to have been a key player in Komen's decision to end its long-standing ties with Planned Parenthood, given her opposition to abortion.
She had been hired by Komen to be its vice president for public policy and chief lobbyist in Washington.
But in her letter of resignation, Handel said the decision to cut funding was not based "on anyone’s political beliefs or ideology," according to an excerpt in the Atlanta Journal-Constitution newspaper.
She said the way Komen gives money to other organizations had been revised before she joined the foundation, and the decision to halt funding to Planned Parenthood had been vetted at all levels.
"I am deeply disappointed by the gross mischaracterizations of the strategy, its rationale, and my involvement in it," she wrote in her emailed letter to Brinker.
"I openly acknowledge my role in the matter and continue to believe our decision was the best one for Komen’s future and the women we serve."
Last week's very public row drove in nearly $3 million in donations for Planned Parenthood in a matter of days, before Komen backed down and apologized, pledging to continue its funding.
Planned Parenthood is the biggest single abortion provider in the United States, especially for low-income women, while Komen has been a leader in the fight against breast cancer with its high-profile "pink ribbon" campaigns.
Komen had initially said it would cease funding because Planned Parenthood was under investigation, and new rules agreed by the charity's leadership allowed it to stop issuing grants to groups in such cases.
The probe was by a Republican lawmaker from Florida, Cliff Stearns, who launched an inquiry into Planned Parenthood over how it handled federal funds and whether such money was used for abortions, which would be illegal.
The ensuing row saw an outpouring of support for Planned Parenthood, with 10,000 supporters -- including New York Mayor Michael Bloomberg and Tour de France cyclist and cancer survivor Lance Armstrong -- coming forward to help.
Komen reversed its decision on Friday, as Planned Parenthood alleged that the foundation had been the victim of what it called "political bullying" on the part of anti-abortion activists.
In her statement Tuesday, Brinker said: "We have made mistakes in how we have handled recent decisions and take full accountability for what has resulted, but we cannot take our eye off the ball when it comes to our mission."
She added: "The stakes are simply too high and providing hope for a cure must drive our efforts."
