(Updates with charges filed)

By James Vicini and Jane Sutton

WASHINGTON/MIAMI, Feb 26 (Reuters) - U.S. criminal charges were filed on Thursday against Ali al-Marri, a suspected al Qaeda "sleeper" agent held for 5 1/2 years at a military prison in South Carolina, sources involved in the case said.

The decision to move the Qatari national into the U.S. court system represents a shift under President Barack Obama. The Bush administration had argued the president had the power to order his indefinite detention without charging or trying him.

The case has been watched closely for clues on how the Obama administration will prosecute some of the terrorism suspects held at the U.S. military prison camp at Guantanamo Bay in Cuba.

Marri is the last of three terrorism suspects held in the United States without charges as an "enemy combatant." He has a case pending before the Supreme Court challenging his indefinite imprisonment without charges.

One of Marri's lawyers, Andrew Savage, said a federal grand jury in Peoria, Illinois, had returned a criminal indictment on Thursday but that it was sealed.

"I have been told unofficially that it has been returned," Savage said.

Two other sources said the charges would be made public on Friday. They were expected to include conspiracy and providing material support for terrorism.

In one of his first acts after taking office last month, Obama ordered U.S. government lawyers to review Marri's case. The same day, he ordered the closing within a year of the Guantanamo prison, which holds about 245 terrorism suspects.

A Justice Department spokesman declined comment on whether charges were being brought against Marri.

LAWYER WANTS SUPREME COURT INVOLVED

Jonathan Hafetz of the American Civil Liberties Union, the lead attorney representing Marri, said, "If this is in fact true, this is something that should have happened seven years ago."

"In the United States it is illegal to detain people indefinitely without charge," Hafetz said. "It is the right step but it is imperative that the Supreme Court review the case and make clear that this is illegal so it never happens again."

Marri entered the United States on Sept. 10, 2001, and was said by a captured al Qaeda member to have come to help operatives plotting a second wave of attacks after the hijacked plane attacks on Sept. 11.

A legal U.S. resident, Marri was initially detained in December 2001 in the investigation of the Sept. 11 attacks.

He was later indicted in Illinois, where he had attended school, for credit card fraud, making false statements to the FBI and other charges. Marri pleaded not guilty.

The U.S. government dropped the criminal charges in June 2003, when then-President George W. Bush designated Marri an enemy combatant and he was taken to the military prison in Charleston.

Only two others have been held as enemy combatants inside the United States since the Sept. 11 attacks.

In January 2006, Jose Padilla, held for three years at the same brig in Charleston, had his case transferred to a criminal court in Miami, where he was convicted on charges of offering his services to terrorists.

Yaser Esam Hamdi, another U.S. citizen held at the brig for two years, was deported to Saudi Arabia after the Supreme Court in 2004 upheld his right to challenge his detention.

The arguments before the Supreme Court are scheduled in Marri's case on April 27. The Obama administration will take the position the criminal charges make his case moot, one source said. (Reporting by Jane Sutton in Miami, Randall Mikkelsen and James Vicini in Washington; Editing by Peter Cooney)

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