Regulators have determined that North Carolina Children’s Hospital is in compliance with federal rules but markedly changed since doctors, department heads and a top administrator expressed concerns three years ago about patients undergoing heart surgery there.

Inspection records released on Thursday cited no deficiencies with the hospital’s operations. But a spokesman for the Centers for Medicare and Medicaid Services, which oversaw an investigation with the state health agency, said the institution’s heart surgery program “is significantly different than it was during 2016-17.”

The North Carolina secretary of health had called for the investigation after a May article in The New York Times gave a detailed look inside the hospital during those years. In secret audio recordings provided to The Times, cardiologists grappled with whether to keep sending patients to their own hospital for surgery and pressed administrators to provide mortality data they said they had not been able to get for several years.

The health secretary dispatched investigators from the state’s Division of Health Service Regulation. They were on site at the hospital for about two weeks in June and later conducted interviews with doctors before preparing a report for federal regulators.

State regulators are authorized to act on behalf of the federal government, performing inspections to make sure hospitals meet certain health and safety standards. Failing to meet those standards can put an institution’s Medicare and Medicaid payments at risk.

The C.M.S. spokesman said investigators looked at patients’ medical records and other documents, conducted interviews with current and former staff members and patients’ relatives, and observed operations at the hospital.

Inspectors concluded that the heart surgery program was substantially different from years earlier, the spokesman said, though he would not provide additional details.

UNC Health Care, which runs the state-owned hospital and is affiliated with the University of North Carolina, has defended its surgery program, describing it as “very strong” today while denying any past problems affecting patient care.

Administrators told The Times that hospital leaders had conducted a “thorough internal investigation” of the pediatric heart surgery program in 2016, determining that “criticism of the program was found to be unsubstantiated.” They attributed any perceived problems to “a dysfunctional group” in 2016 that sowed mistrust and created “team culture issues.”

The hospital system said on Thursday it had nothing more to add.

After the article was published, UNC temporarily suspended its most complex heart surgeries — a measure some doctors had urged years earlier — and introduced several initiatives to “restore confidence” in the program, including creating an external advisory board made up of medical experts from other hospitals.

The hospital also committed to publicly releasing its mortality data for pediatric heart surgery going forward, something it had refused to do in past years. At one point, the data was not available even to cardiologists, who said they wanted it to help them decide where to refer patients. The hospital has said it did not have the information at the time.

UNC Health Care eventually released its past mortality data two weeks after The Times’s investigation — and after a yearlong legal battle in which The Times sued to get the information it had sought under the state’s open records law. The hospital system and the university have since agreed to pay The Times’s legal fees as part of a settlement in the case.

The data showed that the death rate at UNC was especially high among children with the most complex heart conditions — nearly 50 percent.

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