The revelation came in a recovery plan submitted to lawmakers in Washington this week that included an estimated price tag of $139 billion, nearly 50 percent more than the bankrupt US territory requested last November.
A June government report showed that in the four months after Hurricane Maria, the island registered 1,427 more deaths than in the same period the previous year. It did not link the deaths to natural disasters.
Wednesday's report to Congress made the connection.
"The Government of Puerto Rico revealed that there were 1,427 more deaths in the four months after the hurricanes than normal (based on the previous four years)," it said.
Several mainland US media outlets described the report as Puerto Rico finally, but quietly, acknowledging a higher death toll from the devastating storms.
But the island's government denied such a recognition occurred.
The figure released in June, and republished Wednesday, "was not the result of an independent study: it is simple mathematics," the governor's office said Thursday.
"This is not the official number of deaths attributable to Hurricane Maria," it said, adding they were anticipating official results of a George Washington University study in the coming weeks.
Harvard University, in a study released in May, estimated that more than 4,600 may have died as a result of Hurricane Maria.
It said the storm's aftermath, in which larges swathes of the island lost power, basic utility services collapsed and the health care system faced massive disruptions, imperiled the lives of residents.
Eleven months on from Maria, which devastated Puerto Rico just two weeks after Hurricane Irma ravaged the island, its government has yet to update the official toll of 64.
The latest revelations prompted reactions from several Democratic lawmakers, who revived their criticism of President Donald Trump for having downplayed the disaster's magnitude.
"This tragic loss of life of our fellow citizens in Puerto Rico is unconscionable," Senate Minority Leader Chuck Schumer said Thursday.
"We must do more to both hold this administration accountable for a terrible response and help Puerto Rico recover, rebuild and thrive again."
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