The federal government will penalize Maine Medical Center in Portland and five other Maine hospitals for having high rates of infections and other patient injuries.

Mercy Hospital in Portland, which had been on the list of hospitals that were rated fairly poorly when a preliminary report was released in June, will escape any penalties.

The other Maine hospitals facing penalties are St. Mary’s Regional Medical Center in Lewiston, Eastern Maine Medical Center in Bangor, MaineGeneral Medical Center in Augusta, Inland Hospital in Waterville and The Aroostook Medical Center in Presque Isle.

Nationally, 721 hospitals will be lose an estimated $373 million in federal funds, the harshest ever penalty that the government has issued against hospitals for making procedural mistakes that lead to injuries, such as broken bones, and complications, such as infections from catheters, blood clots and bed sores.

The federal Centers for Medicare and Medicaid Services will lower Medicare payments to these hospitals by 1 percent over the fiscal year that ends on Sept. 30, 2015.

The federal government in June issued a preliminary report that identified 761 hospitals nationally that had high rates of complications and infections in an ongoing review that started in 2011. Mercy Hospital had been identified as one of those hospitals, but in the final report it was removed from the list of hospitals sanctioned.

Dr. Scott Rusk, chief medical officer at Mercy Hospital, said the preliminary report released in June was based on inaccurate data and Mercy officials knew their hospital was not in danger of being penalized.

“We knew we were going to be fine because we did a whole lot of work over four years. We are glad the final data came out,” said Rusk.

The Aroostook Medical Center in Presque Isle was not identified in the preliminary report but was added to the final report. It received a high score for urinary tract infections associated with catheters.

Dr. Josh Cutler, vice president of quality and safety at Maine Medical Center, would not say how much the hospital is being penalized but described the amount as “significant.”

The report did not indicate the penalty for each hospital.

Cutler said the hospital has been aware of the quality and safety issues identified by the federal government and has made significant improvements.

“We have been working very hard on these and other areas,” he said.

Medicare judged hospitals on three measures: the frequency of central-line bloodstream infections caused by tubes, infections from tubes placed in bladders, and complications that often occur in hospitals, such as surgical cuts, tears and reopened wounds. Medicare tallied that and gave each hospital a score on a 10-point scale. Hospitals with a total score above 7 were penalized.

Maine Medical Center received a score of 10 – the highest possible score – in all three categories.

St. Mary’s Regional Medical Center during the time of the study had a number of very sick patients, which led to an unusually high number of blood stream infections, said Russ Donahue, director of marketing. He said the hospital will have no issues when the report comes out next year, and he hopes the report does not cause the public to become concerned about the high quality of care at the hospital.

Many of the hospitals listed in the report are larger hospitals and teaching hospitals, such as Brigham and Women’s Hospital in Boston, which are more likely to treat patients with more complex illnesses than are small hospitals.

The penalties come as the hospital industry is showing some success in reducing avoidable errors, according to Kaiser Health News. A recent federal report found the frequency of hospital mistakes dropped by 17 percent between 2010 and 2013.

Staff Writer Beth Quimby contributed to this report.