In this Oct. 22, 2018, photo U.S. Immigration and Customs Enforcement agents surround and detain a person during a raid
FILE - U.S. Immigration and Customs Enforcement agents surround and detain a person during a raid in Richmond, Va.

WASHINGTON - U.S. federal agents will begin collecting DNA samples from hundreds of thousands of immigrants who enter the United States illegally and are held in custody, launching a sharp expansion of a genetic marker collection program created by Congress more than a decade ago, officials announced late Thursday.

The Department of Homeland Security had long exempted immigrants from a 2005 law that requires the collection of DNA samples from "individuals who are arrested, facing charges, or convicted or from non-United States persons who are detained under the authority of the United States." ??

But the Justice Department last August proposed a rule change to eliminate one of four Obama-era exemptions given to immigrants whose DNA samples could not be collected because of a lack of resources. ?

The new rule, which goes into effect on Monday, will allow agents to collect DNA from immigrants who cross the border illegally and are held at immigration detention facilities around the country. In fiscal year 2019, Customs and Border Patrol reported nearly 860,000 illegal border crossings. ?

Documented immigrants and immigrants held at sea or at ports of entry will not be affected. ?

The DNA records collected from detained immigrants will be relayed to the FBI Laboratory in Quantico, Virginia, for entry into its Combined DNA Index System (CODIS) database, ?which is used by local and federal law enforcement agents to link violent crimes. ? ?

Civil liberties groups sharply criticized the new rule, saying it targets a segment of the U.S. population that already feels vulnerable amid a broader crackdown on illegal immigrants. ? The American Civil Liberties Union called it a “xenophobic program.”

"Collecting the genetic blueprints of people in immigration detention doesn't make us safer — it makes it easier for the government to attack immigrant communities, and brings us one step closer to the government knocking on all of our doors demanding our DNA under the same flawed justification that we may one day commit a crime,” Naureen Shah, senior advocacy and policy counsel with the American Civil Liberties Union, said in a statement. ?

Seeking to allay concerns raised by the move, a DOJ official said in a press call with reporters late Thursday that the DNA would not be used by immigration officials.

"The collection of this DNA is only for the purpose of the FBI’s CODIS database, it’s not for any other purpose,” the official said speaking on condition of anonymity. ?

Other Justice Department officials said the will help law enforcement agents identify criminals.

"Today’s rule assists federal agencies in implementing longstanding aspects of our immigration laws as passed by bipartisan majorities of Congress,” Deputy Attorney General Jeffrey A. Rosen said ?in a statement. “Its implementation will help to enforce federal law with the use of science.”

Congress passed the DNA Fingerprint Act in 2005, giving the attorney general the authority to collect records. The departments of Justice and Homeland Security later agreed to a set of exceptions for immigrant detainees.

The Justice Department moved to change the rules last year, after a whistleblower complained to a government watchdog that U.S. Customs and Border Protection (CBP) agents had long evaded the law as a result of the exemption.

The watchdog, Special Counsel Henry J. Kerner, found that "CBP’s noncompliance with the law has allowed criminal detainees to walk free.”

"Given the significant public safety and law enforcement implications at issue, I urge CBP to immediately reconsider its position and initiate DNA collection from criminal detainees,” Kerner wrote in a letter to the White House. ??

The new DNA collections will vastly expand the FBI lab’s database. ?The Justice Department says the lab has the capacity to handle the additional records from DHS and to scale up to meet additional demand.?

A DHS officials said the agency has been collecting DNA samples from immigrants under a pilot program launched in January. ?Under a separate three-month pilot program rolled out last year, immigration agents collected DNA samples from immigrants at the U.S. Mexico border. ?The- acting Homeland Security Secretary Kevin McAleenan later claimed that the agency had uncovered dozens of cases of false parental claims using DNA testing. ?