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The Veterans Affairs administration failed to seriously investigate multiple complaints of poor patient care at the Manchester VA Medical Center in New Hampshire until media reports last year made the issues public, according to a sharply critical letter a whistle-blower agency sent to President Trump.

Doctors at New Hampshire’s only hospital for veterans had long complained that an extraordinary number of veterans being treated in Manchester were suffering from a rare spinal condition that can lead to paralysis if not treated. They said it was a sign hospital officials were not paying attention to patients’ declining conditions until it was too late.

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But for months, VA investigators rebuffed criticisms of the hospital’s care for spinal patients as well as other shortcomings — including chronic flies in one operating room — until the Globe published its story in July, according to a letter from the federal Office of Special Counsel, which investigates whistle-blower complaints.

“This sends an unacceptable message to VA whistle-blowers that only the glaring spotlight of public scrutiny will move the agency to action,” wrote the head of the whistle-blower agency, Henry Kerner, in the Jan. 25 letter to Trump.

VA Secretary David Shulkin’s office released a statement on Thursday saying that it disagreed with the report’s claim it was slow to address the concerns.

Within hours of the story’s publication in July, Shulkin removed the top two leaders in Manchester and announced a “top to bottom review.” He has also promised an additional $30 million in funding.

“As soon as the allegations highlighted by the [Office of Special Counsel] reached Secretary Shulkin, VA took a number of immediate actions to respond rapidly to the issues raised,” said spokesman Curtis Cashour.

Kerner said the VA’s failure to correct problems in Manchester reflect a broader failure to ensure quality care for the 9 million veterans treated at VA facilities each year.

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“These cases are representative of VA’s ongoing difficulties in providing appropriate and expeditious patient care and appear to demonstrate issues with VA’s efforts to ensure allegations are appropriately reviewed,” Kerner wrote. He complained that the VA officials who review patient care complaints were “frequently evasive in their reluctance to acknowledge wrongdoing.”

“None of this comes as a surprise to me,” said Dr. Stewart Levenson, Manchester’s former chief of medicine, who retired last summer. “Agencies cannot investigate themselves. We’ve been saying that since day one. We will never get honest investigations until these investigative bodies are set apart from the agencies they are supposed to investigate.”

US Representative Annie Kuster of New Hampshire, a member of the House Veterans’ Affairs Committee, called Kerner’s letter “damning,” adding that “it’s clear that a more independent investigation is necessary to identify what went wrong at the Manchester” hospital.

The Office of Special Counsel began looking at the Manchester VA in September 2016, when 11 employees, including eight doctors, reported a host of problems to the agency. The investigation ultimately focused on three allegations: that there were flies in an operating room, that a doctor cut and pasted patient medical notes without updating their conditions, and that nearly 100 Manchester patients were suffering from serious spinal problems that were preventable.

The whistle-blowers included Levenson, an 18-year veteran of the hospital, who agreed to speak out publicly after years of fruitless internal complaints.

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“I have never seen a hospital run this poorly — every day it gets worse and worse,” Levenson told the Globe in 2017.

In January 2017, Kerner’s office found a “substantial likelihood” the allegations were true and ordered the VA’s Office of the Medical Inspector to investigate more thoroughly.

The Office of Special Counsel has no authority to investigate on its own and is required to ask the agency in question to conduct an investigation.

But in a report issued in June, the VA’s medical inspector concluded that, although Manchester staff had made mistakes in patient care, no patients were harmed as a result.

In Thursday’s letter, Kerner found that the Office of Medical Inspector report “contained internally inconsistent conclusions at odds with the information” collected during their own investigation.

For example, the medical inspector’s office found that 20 percent of spinal patients at Manchester were not seen in a timely manner, but that it was “unable to substantiate” claims that delays may have harmed patients.

They claimed that 74 of the 97 spinal patients they reviewed received proper care — even though they were still waiting for the results of an outside review.

Kerner said the VA investigators’ findings were “flawed” regarding Dr. Muhammed Huq, the former spine clinic director at Manchester, who for years cut and pasted patients’ medical histories in computer records instead of updating them as the patients’ conditions changed. The whistle-blowers said Huq’s inattention to spinal patients could have allowed their spinal myelopathies to worsen, but the medical inspector concluded no patients were harmed by Huq’s practice.

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“Despite this long-established history of misconduct, investigators determined that there were no adverse patient outcomes attributable to this practice, “ Kerner wrote.

The medical inspector chose not to investigate another serious allegation — that doctors had to cancel surgeries after they discovered dirty and potentially contaminated surgical instruments — because the allegations were not contained in the original referral letter from the Office of Special Counsel to the VA.

“It further demonstrates a myopic approach that could potentially cause harm by ignoring allegations of substantial and specific dangers to public health and safety,” Kerner wrote.

The whistle-blowers were especially angry that the Office of Medical Inspector did not substantiate their most serious allegation: that the severe spine problems of dozens of patients were caused by “clinical neglect,” as alleged by the head of the VA’s spinal cord clinic, Dr. William “Ed” Kois.

The investigators said most of them were treated appropriately and “without delay.”

But the whistle-blowers’ lawyer, Andrea Amodeo-Vickery, said the investigators asked Manchester VA administrators whom they should interview, allowing the officials to select witnesses who were not impartial. The investigators never spoke with a New England Baptist Hospital doctor who, after treating several Manchester spinal patients, wrote this damning assessment to Dr. Kois in 2014:

“Only in 3rd World countries is it common to see patients end up as disabled from myelopathy as the ones who have been showing up after referral from you.”

Kerner’s letter was sent to the president, as well as to the chairmen and ranking members of the Senate and House committees on Veterans’ Affairs.

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His office, which has asked the VA to review the medical records of all the Manchester patients with spinal myelopathies, will request periodic updates and findings when the reviews are completed, the letter said.


Andrea Estes can be reached at andrea.estes@globe.com.