The American Medical Association lost 5 percent of its membership last year as the physician group faced fallout from its endorsement of Obamacare and refusal to retreat from the law’s most controversial provisions.

As physicians and medical school students back away from the well-known organization, they’re turning to upstarts like Docs4PatientCare and the Benjamin Rush Society, two alternatives to the AMA.

Docs4PatientCare maintains contact with about 4,000 physicians who are primarily concerned about preserving the doctor-patient relationship. Many of them became active after the AMA’s endorsement of Obamacare in 2009. That endorsement was touted by President Obama and liberals in Congress to build support for the Patient Protection and Affordable Care Act.

The Benjamin Rush Society has 13 chapters across the country, mostly at medical schools. It was created to offer an alternative perspective to government-run health care. The group’s members include medical students, residents, fellows and doctors.

Both groups are an alternative to the AMA, which has watched its membership erode in recent years. The recent one-year decline of 12,000 members is the latest indication of the AMA’s waning influence.

Even at the height of the Obamacare debate, the AMA represented only 17 percent of physicians in America. Of those members, about one-third are in training (residents or students) and a number are retired or in academic medicine. Physicians pay $420 to be an AMA member.

Dr. Mark Neerhof of Chicago attributes the AMA’s membership decline to the organization’s increased political activity — a change that began when the AMA secured exclusive rights from the government to publish medical billing codes. As that cozy relationship with the government blossomed, the AMA lost focus of representing physicians, Neerhof said.

Docs4PatientCare is filling that void. Neerhof, an executive board member, joined the group during the Obamacare debate when he wanted to better understand the implications of the law and educate other physicians about its impact on their profession. Dr. Hal Scherz, the group’s founder, was awarded the 2011 Salvatori Prize for American Citizenship from Heritage.

“I am fortunate enough to be a physician and I am fortunate enough to be a part of the greatest health-care system in the world, in the greatest country in the world,” Neerhof said. “I don’t want to see that health-care system destroyed. And that’s what I see Obamacare doing.”

The Benjamin Rush Society has a similar mission. Jeet Guram is one of the organization’s chapter leaders at Harvard Medical School. He’s helped bring market-based ideas to the campus and introduce his fellow students to conservative health policy solutions.

“Many of our speakers offered a direct counterpoint to a liberal point of view we heard in the classroom,” said Guram, who is spending the summer as a fellow at Heritage’s Center for Health Policy Studies. “Through our events, students learned about the benefits of market-based approaches to health reform. We aim to expand the range of ideas in the health policy discussion and to show students that there are reasonable, smart, and innovative scholars with conservative values working on health policy issues.”

At the AMA, meanwhile, some members who haven’t bolted over Obamacare have tried to reform the organization from within. But attempts to do so appear futile. This week at the organization’s annual meeting in Chicago, an overwhelming number of AMA members voted to reaffirm the group’s support for Obamacare’s individual mandate. The final vote was 326-165.

Neerhof said the debate over the individual mandate was a sideshow to the real threat Obamacare poses to the doctor-patient relationship, quality of health care, and financial solvency of America.

“The AMA really doesn’t speak for practicing physicians,” Neerhof said. “We don’t have a voice. And that’s what Docs4PatientCare intends to be — a voice for the practicing physician.”