But increasingly, health policy experts and hospital executives say the penalties, which went into effect in October, unfairly target hospitals that treat the sickest patients or the patients facing the greatest socioeconomic challenges. They say a hospital’s readmission rate is not a clear measure of the quality of care it provides, noting that hospitals with higher mortality rates may also have fewer returning patients.

“Dead patients can’t be readmitted,” Dr. Henderson said.

“We’re using a proxy because it’s a convenient proxy — it’s just not a very accurate proxy,” said Dr. Karen E. Joynt, a health policy expert and co-author of an article critical of the penalties in The New England Journal of Medicine this month. Large academic medical centers and so-called safety-net hospitals are bearing the brunt of the new policy, and the authors warn that the penalties could make it even harder for hospitals struggling to care for those patients with the highest needs. The current policy, the article says, “has the potential to exacerbate disparities in care and create disincentives to providing care for patients who are particularly ill or who have complex health needs.”

The penalties, which apply to rates of readmission after hospitalization for heart attacks, pneumonia and heart failure, are now calculated at 1 percent of hospital payments but will increase to 3 percent by 2015. Medicare also expects to expand the targeted readmissions to include more kinds of hospitalizations, like those for chronic lung disease.

Some hospitals say they have little choice but to incur the penalties, simply because they have other demands. At Boston Medical Center, which serves a high number of low-income patients, efforts to reduce readmissions, including making follow-up appointments and writing out a simple plan of what to do after leaving the hospital, have been successful for Medicaid patients.

But the medical center chose not to immediately expand the program to all patients, including the Medicare patients who would count toward future penalties.

“We make those trade-offs,” said Dr. Stanley Hochberg, the center’s chief quality officer. Medicare’s focus on readmissions “doesn’t necessarily align with our social priorities and medical priorities,” he said. Medicare officials say they have listened to hospitals’ concerns but defend the policy as heading in the right direction. “It’s a very traumatic event to go back to the hospital,” said Jonathan Blum, a senior Medicare official. “I’m personally comfortable with some imprecision to our measures.”

“The ultimate goal is to have these numbers come down,” he said.

Because so many hospital readmissions are tied to social or economic factors, hospitals have a hard time predicting which patients are likely to return, said Dr. Jan Berger, the chief medical officer for Silverlink Communications, a consulting firm. When Marjorie Crear, 66, left Ronald Reagan U.C.L.A. Medical Center after a stroke, she struggled to keep track of her medications and to remember her doctor appointments. Tiffany Phan, a newly hired care manager, helped with those tasks and has also been trying to find public housing with a shower instead of a hard-to-navigate bathtub.