Puerto Rico now says 2,975 people died on the island because of the storm.
A report published in May by the Harvard TH Chan School of Public Health said up to 4,600 people were killed and an investigation published in December by the Center for Investigative Journalism found the actual death toll exceeded 1,000 people.
San Juan Mayor Carmen Yulin Cruz, who has been in a war of words with Trump over the federal response to Hurricane Maria, shot back minutes later Thursday morning.
"I think Puerto Rico was incredibly successful", Trump told reporters Tuesday.
The estimate of almost 3,000 dead in the six months after Maria devastated the island in September 2017 and knocked out the entire electrical grid was made by researchers with the Milken Institute School of Public Health at George Washington University. Delays in restoring power led to more deaths.
But perhaps worst of all is the fact that Trump is using words like "tremendous" and "success" to describe a response to a storm that ultimately killed nearly 3,000 people, more than the roughly 1,800 killed by Hurricane Katrina and about the same number of people who were killed in the terrorist attacks of September 11, 2001.
Numerous deaths in the aftermath of Maria were attributed to power outages, and limited access to heath care and clean drinking water.
Philippines: 10 million people in the path of Mangkhut
Mangkhut is expected to be as strong as Haiyan - a super typhoon that killed more than 6,200 people in the Philippines in 2013. Once the Typhoon enters the vicinity of Philippines on Wednesday afternoon, "Mangkhut" will be named as "Ompong" locally.
Trump said Wednesday that his administration is prepared for Hurricane Florence, a storm barrelling toward the Carolina coastline, and insisted that his administration's widely panned response to the devastation in Puerto Rico a year ago was an 'unappreciated great job'.
Hurricane Maria made landfall in Puerto Rico on September 20 2017.Initial figures from authorities recorded 64 deaths however last month the USA territory estimated the death toll stood at 2,975, making it the deadliest storm to have hit Puerto Rico since the 1899 San Ciriaco hurricane. "I think Puerto Rico was an incredible, unsung success", the president said.
The administration's efforts in Puerto Rico received widespread criticism.
He repeatedly referred to the storm as "Floyd" during the call.