Gov. Andrew Cuomo and his own Health Department are at odds over how many New Yorkers have died from the coronavirus.

The governor on Wednesday reported 25,179 COVID-related fatalities in New York State.

But the state Health Department issued an emergency rule on Wednesday that said more than 32,000 New Yorkers died from the killer bug.

The higher figure would boost the COVID-19 death count in the Empire State by 28 percent.

The Health Department cited the higher death count in an official government publication, the New York State Register.

“With over 412,000 confirmed cases and over 32,000 deaths, as of July 13, 2020, which accounts for approximately 22% of all deaths nationwide, New York State is currently the most impacted state in the nation,” states the Health Department’s stated in the emergency regulation, which requires hospitals to stockpile at least a 90 day supply of personal protective equipment.

Cuomo cited the lower 25,179 figure in a press release – as did the COVID-tracker link on the Health Department’s website.

But the higher figure reported in the Health Department’s emergency rule is in line with the 32,725 COVID-19 deaths in New York State reported by the John Hopkins University’s Coronavirus Resource Center.

The discrepancy comes as Cuomo and Health Commissioner Howard Zucker have been accused of low-balling COVID-19 deaths of nursing home residents. In early May, the Health Department stopped separately reporting the number of nursing home residents who died in hospitals.

The issue flared up at a joint legislative hearing on Monday concerning the coronavirus’ impact on nursing homes and the administration’s response to it.

A top Cuomo aide Wednesday said the lower figure was the accurate one and dismissed the higher 32,000 figure published by the Health Department.

“Our number is the accurate confirmed number,” said Richard Azzopardi, a senior adviser to the governor.

He referred questions to the Health Department about its use of the higher 32,000 fatality figure in the government publication.

Critics said the discrepancy over COVID-19 deaths raises more questions about the Cuomo administration’s credibility in light of its handling of nursing home data.

“It’s obvious that they’re trying to lower the fatality rate. They don’t want to look bad. It’s all about trying to save the reputation of one person – the governor,” said Assemblyman Ron Kim, a Queens Democrat.

“At this point, they have lost credibility about laying out the facts.”

The Cuomo administration’s 25,179 fatality figure counts just confirmed deaths linked to COVID-19. But Mayor Bill de Blasio uses a more expansive figure that includes confirmed and probable deaths.

New York City reports 18,937 deaths and 4,626 suspected coronavirus deaths – for a total of 23,563.