Nearly one in four Georgia hospitals — including several of Atlanta’s best-known medical centers — are being penalized by the federal government for high rates of patient injuries.

Federal health officials reported that 31 of 134 Georgia hospitals, or 23 percent, had a high level of such complications, including infections, blood clots, bedsores and falls.

Thirteen of those have received the Medicare penalties for the past three years, including Emory University Hospital Midtown; Grady Memorial; Piedmont Hospital in Atlanta; Southern Regional Medical Center in Riverdale; WellStar Atlanta Medical Center in Atlanta; and WellStar Kennestone in Marietta.

The hospitals penalized this year will lose 1 percent of all Medicare payments for a year, beginning this past October (the start of the federal fiscal year).

Hospitals have long opposed the penalties and are hoping the incoming Republican Congress will do away with them.

“Data shows hospitals nationwide are making major strides in reducing hospital-acquired conditions,’’ Earl Rogers, president of the Georgia Hospital Association, said in a statement last week. “Yet because the Affordable Care Act mandates Medicare penalize 25 percent of all hospitals, a hospital can make improvements in patient safety each year and still be penalized. Imposing financial penalties regardless of improvement takes necessary resources away from continued patient-safety efforts.

The penalties involve not only payments for patient stays but also will reduce the money hospitals receive to teach medical residents and care for low-income people, reported Kaiser Health News recently.

For the first time, the federal Centers for Medicare and Medicaid Services counted the spread of antibiotic-resistant germs in assessing the penalties, KHN reported.

As Rogers noted, the ACA requires that Medicare penalize the 25 percent that perform the worst on these measures, even if they have reduced infection rates from previous years. That quota is one of the things that the hospital industry finds most objectionable about the penalty system.

“With indications of Congress revisiting the ACA, we look forward to participating in efforts to address this counterproductive measure,” Rogers said.

Hospital-acquired conditions have declined since 2010, the year the ACA was passed. Still, KHN reported, the federal Agency for Healthcare Research and Quality, or AHRQ, estimates there were 3.8 million hospital injuries last year, which translates to 115 injuries during every 1,000 patient hospital stays during that period.

“These issues are at the top of the priority list for health system executives and board members nationwide,’’ said Chris Kane, a consultant for DHG Healthcare in Atlanta. “Historically, clinical quality was ‘pass-fail.’ Now there is transparency with financial consequences.”

Some hospitals could be hurt financially in the future if more patients become aware of the safety data, Kane said. Patients, he noted, could start to avoid hospitals that have been punished for low performance.

Not every hospital faces the Medicare penalties. Specialized hospitals, such as those that treat psychiatric patients, veterans and children, are exempt from the penalties. Also exempt are smaller hospitals with the “critical access” designation, which means each is the only provider in its area.

The 13 Georgia hospitals penalized over all three years of the program joined 228 others nationally, including some famous medical centers, such as the Cleveland Clinic in Ohio; Ronald Reagan UCLA Medical Center in Los Angeles; Northwestern Memorial Hospital in Chicago; and Brigham & Women’s Hospital in Boston.

Andy Miller is the editor of Georgia Health News. Kaiser Health News also contributed to this article.