The figures show that there was an increase of 1,397 deaths on the island during the September through December 2017 compared to the same period the year before.
Hurricane Maria made landfall as a category 4 storm on Sept. 20, 2017.
During the first full month after Maria made land fall, the island say an increase of 683 deaths compared to Oct. 2016.
The report does not indicate which of the September 2017 deaths occurred before Maria struck nor did the agency provide location, cause or ages of the dead.
The document released Friday also indicates there were an additional 209 deaths on the island during the next three months, January through March of 2018, compared with the first three months of 2017.
In a statement, Wanda Llovet Diaz, the director of the Demographic Registry said "The public information on fatalities was consistently provided in accordance with the public policy of transparency."
Earlier this week, researchers at the Harvard T.H. Chan School of Public Health estimated that between Sept. 20 and Dec. 31, there were 4,645 "excess deaths," according to the report in the New England Journal of Medicine. The government's official death toll currently stands at 64.
The report relied on household surveys to generate the estimate, which researchers said had a margin of error of plus or minus 3,852, meaning the actual number of deaths could be as low as 793 or as high as 8,498. However, they say about 5,000 is a likely figure.
The number of lives claimed following Maria remains something of a mystery on the island. A team from George Washington University is currently leading an independent effort, commissioned by the island's government, to count the dead. Dr. Lynn Goldman, dean of the Milken Institute School of Public Health, told ABC News the task of counting the deaths is an exhausting one that involves interviewing people involved in the care of those who passed away.