The Puerto Rico government said it "always expected the number to be higher than what was previously reported".
The official death toll stands at 64.
But experts say an accurate count was complicated by the widespread devastation wreaked by the storm.
Carlos Mercader from Puerto Rico's Federal Affairs Administration said he welcomed the Harvard survey.
"The magnitude of this tragic disaster caused by Hurricane Maria resulted in many fatalities," he said.
He added that the island's authorities had also commissioned George Washington University to study the number of deaths and these findings would be released soon.
"Both studies will help us better prepare for future natural disasters and prevent lives from being lost," he said.
The Harvard researchers said interviews conducted in Puerto Rico suggested a 60% increase in mortality in the three months after the storm.
They contacted more than 3,000 randomly selected households between January and March this year and asked about displacement, infrastructure loss and causes of death.
More about: Hurricane
