The government allowed 911 bodies to be cremated without being physically examined by a government medical officer to determine if they should be included in the official death toll from the storm, BuzzFeed News reports.
Each cause of death was listed as being of "natural causes."
As such, the official death toll likely fails to take account of all those who died as a result of the deadly hurricane.
Accurate information about the death toll is important because it allows victims' families to claim federal relief aid.
It has also been used as a measure of how effective relief efforts have been.
When President Donald Trump visited the US territory, he boasted about the low death toll, which at the time was just 16.
Later, when asked to rate the White House's response, he said: "I'd say it was a 10."
Puerto Rico's Department for Public Safety has said deaths would only be added to the official toll if confirmed by the Institute of Forensic Sciences.
The 911 cremations had been permitted to go ahead after the institute reviewed the records, but the bodies were not examined by a government medical officer, a spokeswoman for the department told BuzzFeed.
Several funeral home and crematorium directors told the site they had received no official guidance instructing them to send suspected hurricane victims to the institute. The government said it had issued no such guidance.
Some said they considered heart attacks and people who died of lack of oxygen because of lack of power as hurricane-related deaths, while others said they considered those "natural causes."
Roughly 70 per cent of the US territory remains without power more than a month after Maria struck on 20 September as a Category 4 storm with winds of up to 154mph (245kph).
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