ALBANY, N.Y. — For most of the past year, Gov. Andrew M. Cuomo has tried to brush away a persistent criticism that undermined his national image as the man who led New York through the pandemic: that his policies had allowed thousands of nursing home residents to die of the virus.
But Mr. Cuomo was dealt a blow when the New York State attorney general, Letitia James, reported on Thursday morning that Mr. Cuomo’s administration had undercounted coronavirus-related deaths of state nursing home residents by the thousands.
Just hours later, Ms. James was proved correct, as Health Department officials made public new data that added more than 3,800 deaths to their tally, representing nursing home residents who had died in hospitals and had not previously been counted by the state as nursing home deaths.
The state’s acknowledgment increased the overall death toll related to those facilities by more than 40 percent. Ms. James’s report had suggested that the state’s previous tally could be off by as much as 50 percent.
The findings do not change the overall number of Covid-19 deaths in New York — more than 42,000, the most of any state — but the recalculation in the number of nursing home deaths illustrates how unprepared the nursing home industry was in the first and deadliest weeks of the pandemic.
Mr. Cuomo, a third-term Democrat, had long dismissed the critiques of his policies governing those facilities as partisan attacks from the Trump administration and other Republican adversaries.
But the report by Ms. James, a fellow Democrat, casts a renewed light on the state’s decision to send nursing home residents who had been hospitalized with the coronavirus back to the nursing homes, a policy that Mr. Cuomo has defended as following federal guidelines.
At the same time, Ms. James’s assertion of an undercount of deaths gave credence to theories that the state may have intentionally played down the number of those deaths to avoid blame.
“This is shocking and unconscionable,” said Assemblyman Richard N. Gottfried, the Democratic chairman of the Assembly Health Committee. “But not surprising.”
The 76-page report, which included critiques of other policies promulgated by the Department of Health and of the behavior of nursing home operators, led to a scramble by Mr. Cuomo’s administration to rebut its assertions, including a lengthy response late Thursday afternoon from the health commissioner, Dr. Howard Zucker.
Dr. Zucker said that the state website had always been clear that deaths it listed did “not include deaths outside of a facility.”
“The word ‘undercount’ implies there are more total fatalities than have been reported,” he said. “This is factually wrong.”
He also asserted that the lack of data on hospital deaths of nursing home residents was due to concern and caution about the accuracy of data that nursing homes supplied — an issue also raised by the attorney general. “D.O.H. does not disagree that the number of people transferred from a nursing home to a hospital is an important data point,” he said.
The new data released by Dr. Zucker puts the total number of deaths connected to nursing homes at 12,743.
Ms. James’s findings would seem to put her in rare conflict with Mr. Cuomo; she was the governor’s preferred candidate after Eric T. Schneiderman suddenly resigned as attorney general in 2018, and she readily embraced Mr. Cuomo’s political backing.
Her report seemed certain to inspire more questions about the handling, oversight and performance of the state’s nursing homes in the early stages of the pandemic. Indeed, on Thursday, Mr. Cuomo’s critics in Washington and Albany had already seized on the attorney general’s report as evidence of his dishonesty, amid calls for Dr. Zucker to resign.
“This is now more than a nursing home scandal,” said Representative Elise Stefanik, a conservative Republican from upstate New York. “This is a massive corruption and cover-up scandal.”
Deaths in nursing homes and other long-term care facilities have accounted for about a third of the nation’s some 430,000 Covid-19 deaths. Federal and state authorities have made vaccinating staff and residents at such facilities a top priority, though that effort has been slower than hoped.
But even as state officials in New York tackle vaccine shortages, the count of deaths in the state’s nursing homes remained a source of controversy. Mr. Cuomo had been accused of obscuring a more accurate estimate of nursing home deaths, because the state’s count only included the number of deaths at the facilities, rather than accounting for the residents who died at a hospital after being transferred there.
For its report, Ms. James’s office surveyed dozens of homes and found consistent discrepancies between deaths reported to the attorney general’s investigators and those reported to and officially released by the Health Department.
In one instance, an unnamed facility reported to the Health Department that it had 11 confirmed and presumed deaths on site through early August. The attorney general’s survey of that same facility, however, found 40 deaths, including 27 at the home and 13 in hospitals.
Another facility reported one confirmed and six presumed Covid-19 deaths to the Health Department, according to the report. The attorney general’s office, however, said the facility reported to its investigators that there were more than four times that number — 31 dead — by mid-April.
The attorney general’s report also scrutinized immunity provisions granted to health care providers codified by Mr. Cuomo in the state budget. The report said the protection of immunity may have prompted some nursing homes to make financially motivated decisions at the height of the pandemic, like admitting patients even when the facilities were facing staff shortages or were unequipped to care for them.
Indeed, Ms. James’s office is still investigating and weighing legal action stemming from complaints made to her office about shortcomings and neglect that may have placed residents at risk. Those include allegations of nursing homes that failed to isolate Covid-19 patients, maintain stockpiles of personal protective equipment, properly screen employees for the virus or ensure adequate staffing levels even before the pandemic.
The report also cast a critical eye on perhaps the governor’s most criticized decision since the beginning of the pandemic last year: a March 25 directive from the Health Department that ordered nursing homes to accept and readmit patients who had tested positive.
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The Health Department responded in July with a report that sought to absolve the state from any blame resulting from the March directive. The report concluded that most of the patients sent back to nursing homes “were no longer contagious when admitted and therefore were not a source of infection.” The Health Department concluded that the virus was instead spread by employees who did not know they were contagious.
While acknowledging that Mr. Cuomo’s memo to nursing homes was consistent with federal guidance, the attorney general’s report said the governor’s policy “may have put residents at increased risk of harm in some facilities.” Under the policy, some nursing homes stopped testing residents for the coronavirus, a factor that might have obscured data reported by the facilities, the report found.
For its part, the Health Department also cited Ms. James’s findings on the March 25 memo, saying the report had found no evidence that the policy outlined in the directive “resulted in additional fatalities in nursing homes.”
Ms. James’s report also found a number of homes that “failed to comply with critical infection-control policies,” including failing to isolate residents who had tested positive for the virus or screen employees for it.
The state’s reporting of nursing homes deaths has been the focus of a lawsuit by a conservative economic think tank, the Empire Center for Public Policy, which has sued, seeking to force the Health Department to release more complete data.
Last year, the Democratic-controlled Legislature held hearings partly in an attempt to pry the data from the administration, to no avail.
Dr. Zucker was supposed to testify next week during a state budget hearing, where lawmakers were expected to press him on nursing home deaths, but his appearance was recently pushed back to late February.
The Democratic chairman of the investigations and government operations committee in the State Senate, James Skoufis, who has accused the Health Department of stonewalling investigators, suggested on Thursday that he would use a subpoena to compel the release of data from Dr. Zucker’s office.
“The D.O.H. commissioner’s unresponsiveness to the Legislature’s many questions and concerns is insulting and unacceptable,” the senator said in a statement.
The attorney general asked 62 nursing homes — about a tenth of the state’s total — for information about on-site and in-hospital deaths related to the virus; investigators then cross-referenced that information with public reports of deaths issued by the Health Department. The deaths reported to the attorney general’s office at most of those facilities totaled 1,914, compared to the state’s much lower count of 1,229.
Ms. James said that her office was investigating those circumstances “where the discrepancies cannot reasonably be accounted for by error or the difference in the question posed.”
The attorney general said she was continuing to conduct investigations of more than 20 nursing homes across the state that “presented particular concern,” noting that “other law enforcement agencies also have ongoing investigations relating to nursing homes.”
Under normal circumstances, the attorney general’s office “would issue a report with findings and recommendations after its investigations and enforcement activities are completed,” Ms. James said in her report. “However, circumstances are far from normal.”
Mihir Zaveri contributed reporting.