Veterans Affairs Secretary David J. Shulkin on Wednesday announced an overhaul of the senior leadership overseeing almost two dozen troubled hospitals across the country following the release of a searing investigation into what the agency watchdog said were management failures that put patients at VA’s flagship medical center in the District at risk.

Shulkin said one senior regional official has been reassigned and two others retired as the agency cleans up management of large hospitals and clinics in the Washington area, New England, Phoenix and parts of California. He also said he has appointed 24 new facility directors in the last year, including in Maryland and Virginia, after outside teams identified low-performing hospitals.

“It is time for this organization to do business differently,” Shulkin said at a news conference at the Washington Medical Center. “These are urgent issues, and many of these issues are unacceptable.”

The personnel moves came as Shulkin tries to reassert control over the second-largest federal agency in the aftermath of a separate, critical report by Inspector General Michael J. Missal on a trip Shulkin took to Europe last summer. That report exposed deep factions in the agency’s senior leadership ranks, with Shulkin claiming that political appointees on his staff are trying to oust him.

Missal’s investigation of VA’s Washington Medical Center brought new attention to Shulkin’s leadership even as he announced he is cleaning house.

As a top VA official in the Obama administration in charge of the agency’s massive health-care system, the systemic management failures the inspector general cited occurred on Shulkin’s watch.

The 142-page report found that at least three VA program offices that reported directly to him were aware of “serious, persistent deficiencies” when he ran the Veterans Health Administration in 2015 and 2016.

Shulkin said Wednesday that while the report said managers at the local and regional levels were long aware of the problems, “I was not aware of those issues. I was not aware until Mr. Missal picked up the phone, and I am very much appreciative of that. We took action on the very same day with leadership.”

Shulkin said in the report that he expected any threats to patient safety or operational problems to be raised through the “usual” communication process, meaning they would start at the local level and filter up to the regional office and VA headquarters in Washington.

He said that chain of communication failed.

The report did not address whether Shulkin was directly told of the problems. But it found that despite repeated warnings of systemic failures going back to 2013, leaders at the medical center and its oversight divisions up to senior managers at the veterans health administration largely ignored the problems.

“The dysfunctions . . . were prevalent and deeply intertwined,” the report says. “The [inspector general] encountered a culture of complacency among VA and Veterans Health Administration leaders at multiple levels who failed to address previously identified serious issues with a sense of urgency or purpose.”

“At the core,” Missal wrote, investigators found “an unwillingness or inability of leaders to take responsibility for the effectiveness of their programs and operations.”

He called the “repeated exposure of patients to risk of an adverse clinical outcome,” wasted money and management failures at the medical center “unacceptable.”

Shulkin called the findings in Washington “a failure of every level. It’s unacceptable to me. Fortunately this has not led to any known patient harm.”

“We will have an entire new leadership here in D.C., to make sure this is an environment that is safe for the 93,000 veterans we serve,” Shulkin said.

He described the moves as “the start of a restructuring of VA affairs” and said he believes “the issues here in Washington are happening at VAs across the country.”

Last April, after the inspector general’s office issued a rare alert as investigators began uncovering safety problems at the facility, Shulkin removed the medical center’s director, Brian Hawkins.

Lawrence Connell, installed last year as acting director of the D.C. medical center, said Wednesday he has hired more than 50 nurses and other staff. “It’s a different hospital than it was,” he said.

The hospital and three clinics that make up the Washington Medical Center are among the largest and most complex in VA’s sprawling health-care system.

The center provides care to about 100,000 veterans in the region, among them many members of Congress.

Despite the risks to patients of years of dysfunction, no one died, Missal wrote, a lucky outcome he attributed to actions by some dedicated medical staff, who conducted their own inventories, raced to nearby hospitals to borrow supplies — including during surgeries — and other efforts. The stopgap measures “are not in accordance with an effectively managed health care facility,” he wrote.

Wednesday’s report is the result of a year-long review after a confidential complaint led investigators to conduct an initial inspection in March 2017 and issue their alert three weeks later.

The report describes “widespread and formidable inadequacies” in many of the essential functions that are needed to operate a hospital. VA leaders who failed to correct the conditions told investigators they were not aware of the staffing challenges or the scope of the problems, claims the inspector general said did not ring true.

Some senior leaders also told investigators that since the problems did not lead to patient deaths or injuries, they did not feel an urgency to act.

Among them were a nonfunctioning system of inventory practices that led to a breakdown in tracking medical supplies, equipment and instruments so they could be delivered to operating rooms and other patient care areas. As a result, “veterans were put at risk because important supplies and instruments were not consistently available in patient care areas,” according to the report.

Data was not entered into the inventory system, and orders were not placed when supplies were low, resulting in shortages. Clinical staff routinely had trouble locating them in storage areas.

Patients were hospitalized needlessly — at great medical risk — when procedures had to be canceled following their admission, sometimes for overnight stays, because equipment could not be accessed for scheduled surgeries.

Some patients received unnecessary anesthesia. Surgeons had to rely on outdated medical instruments. Discolored and broken instruments reached clinical areas because the hospital’s sterile processing operation was broken down.

Investigators also found dirty storage areas for medical supplies and equipment.

In at least one instance, the medical center ran out of bloodlines for dialysis patients and was only able to provide dialysis service because the medical staff borrowed bloodlines from a private hospital nearby.

According to the report, the medical center failed to properly track instances when patient safety was at risk and ended up minimizing patient safety events.

More than 1,300 boxes of documents, including patient files with confidential information, were stored in unsecured areas, including the hospital’s off-site warehouse, its basement and a dumpster.

Investigators found more than 10,000 open and pending consults for prosthetics and hearing aids, leaving veterans to wait months for these items.

The medical center wasted money, the report alleges. About $92 million in supplies and equipment were charged to government purchase cards over a two-year period without proper controls to make sure the supplies were needed and were cost-effective.

The purchases represented almost 90 percent of the supplies the hospital bought, instead of using approved federal contracts that offer far cheaper prices.

The same items were also ordered multiple times because the medical staff was nervous that supplies might not be available when they needed them for patient procedures.

Missal noted some improvements under the facility’s new leadership. The wait for prosthetics has decreased, and storage rooms are now clean. But the report said problems persist.

Correction: An earlier version of this story said that Shulkin announced plans to replace leaders at about 20 facilities. It has been corrected to say that he has appointed 24 new directors over the last year.