Long before revelations in the spring that the Veterans Affairs hospital in Phoenix had manipulated waiting lists to hide that veterans were facing long delays to see doctors, senior department officials in Washington had been made aware of serious problems at the hospital, according to filings before a federal administrative board.

The documents in the case of the Phoenix hospital director Sharon Helman, who had been contesting her Nov. 24 firing, provided new details of how much officials knew about the medical center, including patient backlogs, shortages of medical personnel and clinic space, and long waiting lists.

The filings included the sworn statement of Susan Bowers, the executive in charge of dozens of hospitals and clinics from West Texas to Arizona, that she had warned her superiors in Washington that if any V.A. medical center was going to “implode,” it would be Phoenix.

Ms. Bowers, who retired one month ahead of schedule in May as the scandal emerged, said that before Ms. Helman became the head of the Phoenix facility in 2012, an audit showed the hospital was out of compliance with a directive requiring patients to be placed on an official electronic waiting list. There was, in fact, no such active list for primary-care patients in Phoenix, even though a previous hospital director had certified compliance, she said.

Ms. Bowers said that when she submitted a report stating that the Phoenix hospital was out of compliance, she was pressured by other officials to say that it was compliant.

She also said that beginning in 2009, she briefed Eric K. Shinseki, then the Department of Veterans Affairs secretary, and other top officials several times a year about the patient backlog and other problems in Phoenix. She said that projects she pushed — like improving the scheduling system or adding clinic space in Phoenix so more patients could be seen — were defunded or delayed because, she was told, there was no money, or no legal mechanism to lease space.

Ms. Bowers’s testimony added a dimension to a scandal that shook the confidence of millions of veterans who use the department’s hospitals and clinics and led to the ouster of Mr. Shinseki in May. After a whistle-blower charged that there were secret waiting lists for care at Phoenix, an investigation by the department’s inspector general found that 1,700 patients there had not been placed on proper waiting lists and may never have received medical care. A top official in the inspector general’s office also testified that delays for care had contributed to some patient deaths.

The inspector general’s report faulted Ms. Helman for efforts that “resulted in a misleading portrayal of veterans’ access to patient care.” Before she was placed on leave in May, Ms. Helman denied instructing staff members to create or maintain “secret” waiting lists, telling CNN, “It’s never come from me.”

This week, a federal administrative judge, Stephen C. Mish, found that it was “more likely than not that at least some senior agency leaders were aware, or should have been, of nationwide problems getting veterans scheduled for timely appointments” and that the Phoenix hospital, “as a part of the nationwide system also had those problems.”

He ruled that the department failed to provide sufficient evidence that Ms. Helman should have been fired over the conditions at Phoenix. Still, he upheld her dismissal on separate charges of taking favors from a health care industry consultant.

A V.A. spokeswoman declined to comment on the litigation. Earlier, the department said it removed Ms. Helman “based on the available evidence.”

In filings in Ms. Helman’s case, the department also acknowledged that before April 2014, three high-ranking officials, including a deputy under secretary for health and the associate director for scheduling and access, were aware of issues at Phoenix related to wait times, the electronic waiting list or patient appointment backlogs.

A sworn statement by the former under secretary for health, Dr. Robert Petzel, also stated that before Ms. Helman arrived, the “V.A. was aware of access issues” in Phoenix. Mr. Shinseki, however, according to the filings, said that he was “unable to recall the contents of the briefings” from Ms. Bowers and “did not recall any of the allegations regarding Phoenix being raised during any budget presentation.”

One crucial question remains: Why did senior officials not do more to fix the underlying problem, which was a shortage of doctors and other clinicians while demand for care was soaring? After the appointment of a new secretary this summer, the department abruptly disclosed that it was short 28,000 doctors, nurses and other staff and that some places, including Phoenix, acutely lacked clinic space. It has not been said whether these shortfalls were previously discussed at high levels inside the department or the Obama administration.

Judge Mish’s ruling suggests Ms. Helman was scapegoated, her lawyers say. Seeking to convince people of “its preferred story line” that blamed her and others in Phoenix instead of senior officials, the department purposely made them “bear the brunt of the contrived political outrage,” one of her law firms, Shaw Bransford & Roth, said in a statement, though it did not say whether she planned to appeal.

Her lawyers say they believe the department moved to fire her only after federal criminal investigators discovered emails between Ms. Helman and the consultant and turned them over to the V.A.

The documents are not the first indication that senior officials knew of the Phoenix problems. In 2008, the inspector general found that it was “an accepted past practice” there to alter appointments to avoid waits over 30 days.

Two years later, a deputy under secretary warned regional directors in a memo to eliminate improper practices being used to “improve scores on assorted access measures.” In a telephone interview after the judge’s ruling in the case, Ms. Bowers said that 2010 memo was written after she told the official of scheduling problems in Phoenix.

When she briefed Mr. Shinseki about problems, she added, he would say, “There’s a process, and we need to follow through on the process.”

(The New York Times)