As the sequester axe descends on Medicare this week, some of the pain is falling on programs helping new doctors prepare to set up shop in the neediest neighborhoods — just months before health care reform brings a surge in demand.

Funding for medical residencies in primary care are about to be hit with cuts of up to 8 percent, according to the American Academy of Family Physicians, harming their ability to train recent medical school graduates.

One program set to take a hit is Teaching Health Center Graduate Medical Education. Approved by Congress through 2015, it has made it possible for the Manhattan-headquartered Institute of Family Health to train eight doctors in Harlem and another eight in the Hudson Valley.

Dr. Robert Schiller, senior vice president and chair of graduate medical education at the nonprofit network, called his group’s expected 5 percent reduction in funding a “substantial hit” and worries that it will eat at his core mission: to establish physicians’ practices in underserved communities.

“Organizations that accredit say certain training needs to be met, and they don’t care about the financial issues,” said Schiller. “If you go through a hard time they say, ‘Look, you’re still responsible that doctors are competent.”

The bleeding could get still worse. Federal budget negotiations still underway have yet to determine whether the $230 million program will live beyond its 5-year authorization. Since residency training takes three years to complete, without knowing the future funding picture Schiller remains unsure whether he can enroll a new class of trainees in July.

“We’re stuck,” said Schiller. “And it’s disheartening.”

The doctors coming out of programs like his are badly needed. About 1.2 million Medicaid-eligible New York City residents live in areas considered by the U.S. Department of Health and Human Services to be “medically underserved”, or living in areas where there are more than 3,000 residents to each Medicaid-serving physician.

By October, the state’s health insurance exchange will be up and running, bringing more than 1.1 million currently uninsured to coverage. New York City alone is projected to see an additional 210,000 residents enroll in publicly subsidized insurance, bringing the total in the city to more than 3.4 million.

“The expansion of coverage is going to create a lot more demand for something that was already in short supply,” said Ronda Kotelchuck, executive director of the Primary Care Development Corporation. Kotelchuck helped the city’s Health and Hospitals Corporation pen a 2006 study detailing the extent of the city’s shortage of family doctors.

The city’s primary-care physician shortage isn’t shared evenly across neighborhoods. The Upper East Side has 261 family doctors per 100,000 residents, five times the minimum ratio for adequate care established by the feds. By contrast, the Northeast Bronx has only 34 for the same number of residents.

The shortage is particularly acute among Medicaid-eligible residents of Bedford-Stuyvesant, Brooklyn, where HHS considers more than 158,000 to be medically underserved. The doctor shortage accounts for why the neighborhood has one of the highest rates of avoidable hospitalizations in the city, and why Woodhull Medical and Mental Health Center, at the northern tip of the shortage area, has one of the most frequented emergency rooms in the five boroughs.

Patients like Derrick Williams, 57, simply can’t find primary care and end up at Woodhull.

“I called for an appointment, but something came up and I needed a doctor,” said Williams, with frustration. He’d tried to set up an appointment with his primary care doctor, but the office said he’d have to wait three weeks. So instead, he waited in Woodhull’s emergency room for hours to see a doctor who could address his back pain.

“I don’t prefer to come here,” he said, looking up from his newspaper, “But I have no option.”

Bed-Stuy’s suffering is felt in many other neighborhoods. As of 2009, New York State ranked second to last in avoidable hospital use and costs. And the communities that have the highest rates of avoidable hospitalizations are the same ones with insufficient access to primary care. The city Department of Health and Mental Hygiene found that two out of every five emergency room visits were preventable with adequate primary care, and that minority and low-income residents were the most frequently beset with health problems linked to limited primary care availability.

The state has been pushing to address the problem. Since 2008, it has invested millions through its “Doctors Across New York” program, to support practices and repay student loans for physicians who open up shop or train in medically underserved areas.

In the recent state budget negotiations, Gov. Andrew Cuomo proposed a controversial measure, already being tried elsewhere in the country, that would expand clinical privileges for nurse practitioners, bringing their responsibilities closer to those of physicians. The proposal didn’t make it into the bill, but it’s on the map.

“Physician shortages are real,” said state health commissioner, Dr. Nirav Shah after a recent presentation on the state’s health care. “And the needs of an aging population will only exacerbate the problem.”

New York anticipates a shortage of anywhere between 2,500 and 17,000 physicians by 2030, with as many as 3,153 in the city alone.

Primary care as a career path has been declining in popularity, because medical specialties tend to earn more for a doctor over a lifetime – a de facto penalty as high as $3.5 million for those who choose primary care. When students emerge from medical school saddled with large debt loads, the allure of higher paying positions is hard to turn down.

“Residents that are facing $200,000 in debt, what do I choose economically?” asked Dr. Cain, of the American Academy of Family Physicians.

“Do I choose primary care, which is a wonderfully rewarding career, or being able to do a more limited care specialty?” he said. “People are choosing the lifestyle of reimbursement.”