"We're still helping Puerto Rico", Trump said.
Researchers tracked the number of deaths using death certificates and other mortality data between mid-September 2017 to mid-February of this year.
He's also creating a commission to implement recommendations in the new report, and creating a registry of the people expected to be most vulnerable in a future storm, such as the elderly, bedridden or kidney-dialysis patients.
Puerto Rico Gov. Ricardo Rossello upgraded that count to nearly 3,000 on based on a report commissioned by island officials and conducted by George Washington University's Milken Institute of Public Health.
Trump has come under stiff criticism for his handling of the disaster, principally from Carmen Yulín Cruz, the mayor of Puerto Rico's capital city San Juan. That would make it the deadliest US natural disaster in more than 100 years.
He echoed one finding in the report - that doctors "lacked awareness" on how to appropriately certify deaths attributed to natural disasters. Yes, I made mistakes.
Cruz went on MSNBC on Wednesday shortly after Trump's comments and said the president was "incapable of feeling solidarity and empathy".
US President Donald Trump throws a paper towel roll as he visits the Cavalry Chapel in Guaynabo, Puerto Rico, on October 3, 2017.
In December, public safety officials revised the official count to 64, adding some fatalities newly certified as indirect deaths related to the storm.
The government's initial number was for those killed directly by the hurricane, crushed by collapsing buildings, drowned or hit by flying debris.
If the new figures are accurate, Hurricane Maria is the deadliest storm to have hit Puerto Rico since the 1899 San Ciriaco hurricane. "What can I do?'", said Collazo, executive director of the Defensoría de las Personas con Impedimentos (DPI), a government agency in charge of protecting the rights of the island's disabled.
Puerto Rico's governor on Tuesday raised the USA territory's official death toll from 64 to 2,975 after an independent study.
Researchers estimated the excess deaths with the help of mathematical modeling that compared post-hurricane deaths to the expected number based on historical patterns, and adjusted for age, sex and migration from the island.
"I did was I thought ought to be done as I screamed, literally, out of the top of my lungs to say "We're dying here" and the bureaucracy and the inefficiency of the federal government was killing us".
The current official death toll exceeds Hurricane Katrina's carnage of 1,833 in 2005, but is still short of the deadliest hurricane in recorded USA history.
In May a Harvard University-led research team estimated that 4,645 lives were lost from Maria on Puerto Rico.