The US State Department said that Central Americans and Haitians granted temporary status, some who have lived in the country for 20 years, could now be sent to their home countries.
They had originally been given Temporary Protected Status because their nations had been deemed unstable due to armed conflict and natural disasters.But the Washington Post reported that Secretary of State Rex Tillerson has ruled those conditions no longer apply.
The Department of Homeland Security now has until Monday to announce its plans for about 57,000 Hondurans and 2,500 Nicaraguans whose protections are due to expire.
A large number fled to the US illegally in 1998 as Hurricane Mitch battered Central America and have had their status renewed ever since.
Under the changes, the refugees could be arrested and sported once their protections expire.
So far, the Department of Homeland Security has refused to say what action will be taken.
A decision on the other 240,000 refugees who have the status will be made by January.
Many of them have homes, businesses and children who were born in America.
According to the paper, Donald Trump’s administration has stressed the programme was never meant to allow permanent residency in America.
An official said: "It is fair to say that this administration is interpreting the law, exactly as it is, which the previous one did not.
"It is very clear what needs to be done."
Mr Trump campaigned for the presidency last year on a promise to deport large numbers of immigrants.
Last month, people close to the administration said the White House was considering anti-immigration activists' appeals to pull back on the programme.
And this week, following the truck terror attack in New York that killed eight people, the President urged Congress to end the Diversity Immigrant Visa program under which suspect Sayfullo Saipov entered the United States in 2010.
The diversity program, signed into law in 1990 by President George Bush, was designed to provide more permanent resident visas to people from countries with low US immigration rates.