The revised death toll is nearly 50 times the previous estimate of 64.
Governor Ricardo Rossello "accepted" the findings in a long-awaited independent investigation.
Puerto Rico has struggled to repair its infrastructure and power grid since the storm, and is asking US Congress for $139bn (£108bn) in recovery funds.
"I'm giving an order to update the official number of deaths to 2,975," Governor Ricardo Rossello said at a press conference on Tuesday. "Although this is an estimate, it has a scientific basis."
In a statement, the White House said the federal government supported the governor's efforts to "ensure a full accountability and transparency of fatalities" in last year's hurricane.
President Donald Trump was criticised for praising the federal response to the hurricane-ravaged island in the weeks following the storm. Critics accused him of showing more concern for residents in Texas and Florida after they were hit by hurricanes.
Why the change in numbers?
The authorities have faced nearly a year of criticism for underreporting the true toll of Maria - the most powerful storm to hit the region in nearly 90 years.
Until now, the official figure was 64 - even though the island had previously acknowledged the death toll was probably much higher. In the wake of the disaster, some experts estimated as many as 4,600 deaths.
The government's initial number was arrived at by counting those crushed by collapsing structures, drowned and hit by flying debris.
However many people also died as a result of poor healthcare provision and a lack of electricity and clean water. Repeated power outages also led to an increased number of deaths from diabetes and sepsis.
The latest findings - accepted by the island's authorities - were made in a report by experts from George Washington University, which the governor commissioned.
"This shows the magnitude of the catastrophe," Governor Rossello told newspaper El Nuevo Dia.
When asked why his government was unable to recognise a higher death toll until now, he replied: "I am not perfect. I make mistakes. Now, hindsight tends to be 20-20."
He echoed one finding in the report - that doctors "lacked awareness" on how to appropriately certify deaths attributed to natural disasters.
"The responsibility for adjudicating the cause of deaths rested with the doctors," Mr Rossello told the island's most circulated paper. "But unfortunately there was no formal process to prepare them for this kind of devastation.
"At that moment, that was the number [of deceased] that we had and today we have the evidence which indicates the number was definitely higher."
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