Adithya Sambamurthy/The Bay Citizen

Planned Parenthood, which operates a clinic in this building in San Francisco, will no longer have a presence in several Bay Area counties after punitive action by its parent organization

A financial and administrative meltdown in recent years has led to the end of one of the largest Planned Parenthood affiliates in the United States.

Patients visiting Planned Parenthood’s eight clinics in San Francisco and four other Bay Area counties often encountered wait times exceeding two-and-a-half hours. Shortages of critical supplies, including intrauterine devices, meant some patients were turned away.

Doctors, nurses, midwives and physician’s assistants complained to the national organization about low morale and a hostile work environment at Planned Parenthood Golden Gate, the local affiliate that owned and operated the clinics.

“P.P.G.G. is experiencing major system issues that are affecting the access and quality of patient care that we provide,” warned a 2008 letter from 30 doctors and clinicians detailing these problems to Bay Area administrators and senior officials at Planned Parenthood Federation of America in New York.

On Sept. 3, Planned Parenthood Federation of America will take the rare step of stripping a local organization of its affiliate status, citing financial and administrative problems. The national organization sent a letter in July saying that the affiliate’s conduct might jeopardize patient care and Planned Parenthood’s trademark, said Therese Wilson, the Bay Area affiliate’s interim chief executive. Wilson denied the accusations.

The national organization would not comment on the reasons for disaffiliation.

By the end of this week, there will not be not a single Planned Parenthood clinic in San Francisco, San Mateo, Marin, Sonoma and Alameda Counties.

The care of some 50,000 patients, more than 90 percent of whom live at or below poverty level, is at risk, health care providers in the area say.

Planned Parenthood Golden Gate said it planned to continue to offer the same services in the same facilities, under the name Golden Gate Community Health. Yet tax filings show that the nonprofit lost $2.8 million during the 2008-9 tax year, at the same time its chief executive’s total compensation exceeded $340,000. The organization has not broken even since the 2005-6 tax year, records show.

Patients depend on the Planned Parenthood clinics for birth control, cervical-cancer screening, testing for sexually transmitted diseases and abortions.

“If their services were to be diminished or not be there, clearly that is going to have consequences,” said Juan Vargas, an obstetrician and geneticist at Benioff Children’s Hospital. “There would be a void that would be very difficult to fill.”

The national federation has assigned Planned Parenthood Golden Gate’s five Bay Area counties to neighboring Planned Parenthood affiliates, which are racing to get new clinics up and running.

Interviews with current and former staff members and executives of Planned Parenthood Golden Gate, as well as documents obtained by The Bay Citizen, show a health organization that was unraveling under the strain of financial distress, even as it portrayed itself as a robust institution that attracted high-profile supporters.

Planned Parenthood Golden Gate’s leaders said the organization was undermined by a poor economy and lack of support from the national organization.

“It’s my opinion that the disaffiliation was unnecessary,” Dian Harrison, the longtime chief executive of Planned Parenthood Golden Gate, wrote in an e-mail interview.

Harrison has not led the organization since January 2010, when she went on leave for reasons that she declined to specify.

More than 100 local affiliates pay dues to Planned Parenthood Federation of America, which operates an (800) number and a Web site connecting patients to the clinics in their area. Affiliates use the Planned Parenthood name, as well as the organization’s medical standards, guidelines and educational materials; they get discounts on supplies, like contraceptives, and support with fund-raising.

Planned Parenthood Golden Gate was formed in 1996, when three Planned Parenthood affiliates merged. Harrison led the organization from its inception. The affiliate won performance awards from the national organization in 2003 and 2005. Gloria Steinem appeared at a fund-raiser in 2007, as did Donna Brazile, the Democratic political strategist, in 2008.

One report distributed by the organization included an animated cartoon starring Harrison, who transforms into a “Superhero for Choice” armed with a condom-shooting popgun that scatters anti-abortion protesters.

Harrison won the admiration of wealthy donors and board members, who praised her as an innovative leader whose vision for social justice extended far beyond the Bay Area, even leading her to forge a partnership in Ethiopia to try to improve reproductive health care there.

Planned Parenthood Golden Gate

Dian Harrison, right, with Gloria Steinem

Yet many staff members saw Harrison and her team as out of touch with their daily realities, creating a dysfunctional corporate culture. Some former employees still hold occasional get-togethers dubbed the “P.P.G.G. P.T.S.D. Support Group.”

Financially, Planned Parenthood Golden Gate did not measure up to its public profile. According to a 2007 internal report by the national organization, its finances were the worst among the top 10 largest affiliates in the country. Planned Parenthood Golden Gate failed to meet four out of nine indicators of financial health that year, the report said. Some of those benchmarks — like maintaining 60 days of cash on hand — had not been met for years.

Over the next two fiscal years, the affiliate’s revenues from contributions and grants fell 45 percent, to $2.3 million from $4.2 million. The growing internal crisis affected services, according to medical personnel.

“There were days when patients would come to see if they were pregnant and we couldn’t tell them because we had no pregnancy tests in stock,” said a doctor who no longer works for the affiliate.

In her e-mail interview, Harrison attributed the financial distress to the “downturn in the economy and a dramatic decrease in fund-raising.”

Yet, some aspects of the organization’s poor financial condition remain unclear. Other Bay Area affiliates have weathered the recession. Planned Parenthood Shasta-Diablo, based in Concord, for example, has seen its revenues increase.

This year, Planned Parenthood Golden Gate tried unsuccessfully to interest other Bay Area affiliates in buying some of its clinic buildings or merging, said Wilson, the interim C.E.O.

In the wake of Planned Parenthood Golden Gate’s crisis, some of its health services have already been reduced. In June 2010, its Redwood City clinic closed, and abortion services at some other clinics have been significantly cut back.

Harrison argues that Planned Parenthood Federation of America violated its “own standards of affiliation” by taking “premature action” to sever its ties. Wilson wrote in an e-mail that the affiliate had spent the “past six months trying to resolve our differences” with the national organization.

“There has never been any evidence that P.P.G.G.’s conduct jeopardizes patient care,” Wilson wrote in an e-mail.

Karen Ruffatto, vice president of affiliate services for Planned Parenthood Federation of America, said in a statement that the accreditation process was confidential. The organization “has clear guidelines regarding accreditation issues,” Ruffatto said, “and the decision to reassign the San Francisco service area followed these guidelines.”

Bay Area health care providers hope Planned Parenthood Golden Gate’s patients will still be able to find the care they need.

“There are real consequences to gaps in care,” said Eleanor Drey, a professor of obstetrics and gynecology at the University of California, San Francisco. “I really hope that it’s possible for these women to keep getting services consistently.”

This article also appears in the Bay Area edition of The New York Times.