A Mexican national arraigned last month in San Diego on 11 charges in a rape case is now a poster boy for a new Department of Justice policy requiring federal officials to take DNA samples from those arrested on immigration violations.

Before being charged with rape, suspect Carlos Ceron Salazar was deported nine times from the United States. Had the new DOJ policy been in place, federal officials say many victims could have been spared.

"In the past, we have had a limited authority to take DNA samples," said Elisebeth Cook, an attorney in the Office of Legal Policy at the Justice Department. "It's critical while we have the opportunity to take the sample."

But civil libertarians are concerned about the policy, pointing to backlog of DNA samples already existing in criminal laboratories across the country. Samples will be taken from those who are merely detained, they say, not just from those who arrested or charged with any crime.

"We're now treating people who have yet to be taken to court of law, proven to have violated either the civil or criminal law and engaging in probably the most invasive kind of information gathering we have," said Larry Frankel, an attorney for the American Civil Liberties Union.

Frankel says the new policy will likely lead to increased racial profiling from law enforcement.

"We're going to find people who someone suspects they're not citizens because of their skin color or their accent, when in fact they are naturalized citizens," he told FOX News.

Yet federal officials insist that cheek swab data taken from those detained — whether it be for coming into the country illegally or overstaying a visa — will be a valuable crime-fighting tool. The DOJ says nearly 60,000 cases have been solved using DNA evidence, either aiding in the conviction or the exoneration of suspects.

In cases where a person is wrongly detained, that individual will have a right to petition the Federal Bureau of Investigations to have their DNA sample removed from their databases, a remedy which the ACLU argues is too arduous for a person who never committed a crime in the first place.

The ACLU is looking for ways to fight the policy. While the organization has not filed any legal action, they will not rule out a future lawsuit.