“I don’t think there’s a contradiction between the goals of health care reform and the goals of antitrust,” Ms. Feinstein said in an interview, as she surveyed the wave of mergers, consolidations and affiliations sweeping through the health care industry.

Edith Ramirez, the chairwoman of the commission, said it had challenged fewer than 1 percent of hospital deals. But the message of those cases is reverberating in the health care industry.

In the Idaho case, Federal District Judge B. Lynn Winmill acknowledged that the combination in 2012 of St. Luke’s Health System and the Saltzer Medical Group — the largest independent physician group in the state — was primarily intended to improve care for patients. But, he said, “there are other ways to achieve the same effect that do not run afoul of the antitrust laws.”

Judge Winmill said the combined entity would have a huge share of the market for primary care physician services and could charge higher prices to health insurance plans, which could then pass the costs to consumers by charging higher premiums.

“The Clayton Act is in full force, and it must be enforced,” the judge said, noting that the law bans mergers that may substantially lessen competition. He ordered the hospital system to divest itself of the physician group. The decision is being appealed.

A federal investigation can be an ordeal for hospital executives. “I was shocked at how aggressive the F.T.C. was,” said Randy Oostra, the president of ProMedica, the hospital system at the center of the Ohio case.

Image Deborah L. Feinstein, at the Federal Trade Commission, said the health care law did not repeal the nation’s antitrust laws. Credit... Gabriella Demczuk/The New York Times

Jeffrey C. Kuhn, the general counsel of ProMedica, said: “The government has lots of resources and lots of lawyers. Their attitude was adversarial. Our trustees and top executives had to fly to Washington to be deposed. We were eager to tell our story, but it quickly turned into an inquisition. We turned over millions of pages of documents, at great expense.”