"Our results indicate that the official death count of 64 is a substantial underestimate of the true burden of mortality after Hurricane Maria," the authors wrote.
The official death estimates have drawn sharp criticism from experts and local residents, and the new study criticised Puerto Rico's methods for counting the dead - and its lack of transparency in sharing information - as detrimental to planning for future natural disasters. The authors called for patients, communities and doctors to develop contingency plans for natural disasters.
Maria caused US$90 billion in damage, making it the third-costliest tropical cyclone in the United States since 1900, the researchers said.
More than eight months after Hurricane Maria devastated Puerto Rico, the island's slow recovery has been marked by a persistent lack of water, a faltering power grid and a lack of essential services.
All those issues have imperiled the lives of many residents who have been struggling to get back on their feet, especially the infirm and those in remote areas, some of which were the hardest hit in September.
Counting the dead in such natural disasters is always a difficult task, even under ideal circumstances; in Puerto Rico it was hampered by numerous systemic failures and what the Harvard researchers found was a complex method for certifying the deaths in San Juan.
The researchers noted that the Centers for Disease Control and Prevention says that deaths can be directly attributed to storms like Maria if they are caused by forces related to the event, from flying debris to loss of medical services; in Puerto Rico such deaths continued for months.