By James Vicini

WASHINGTON, Dec 10 (Reuters) - Supreme Court justices voiced concern on Wednesday about including top U.S. government officials in a lawsuit by a Pakistani man claiming abuse while imprisoned in New York after the Sept. 11 attacks in 2001.

They questioned whether Javaid Iqbal, who was held more than a year after the attacks, can proceed with his lawsuit against former Attorney General John Ashcroft and FBI Director Robert Mueller without more evidence to support his claims.

"I don't know on what basis any of these allegations against the high-level officials are made," Justice Antonin Scalia told Alexander Reinert, the attorney arguing for Iqbal.

The Bush administration's top courtroom lawyer, Solicitor General Gregory Garre, argued that Ashcroft and Mueller have immunity, that they cannot be held personally liable and that the lawsuit against them must be dismissed.

The issue before the Supreme Court involved only whether the lawsuit against Ashcroft and Mueller can continue and did not address the claims of mistreatment by other current and former government officials.

Garre said the policy the two top law enforcement officials adopted after the Sept. 11 attacks was to hold the suspects until cleared by the FBI. He denied Iqbal's claim that Ashcroft and Mueller approved of discriminatory acts or misconduct by lower-level officials.

Iqbal, a Muslim, said in the lawsuit he was subjected to verbal and physical abuse and to unlawful ethnic and religious discrimination.

Chief Justice John Roberts expressed doubt to Reinert that the lawsuit against Ashcroft and Mueller can go forward.

"What you have to allege are some facts showing that they knew of a policy that was discriminatory based on ethnicity and country of origin," Roberts said.

Besides Ashcroft and Mueller, Iqbal sued about 30 other current or former U.S. government officials, including the warden at the detention facility and the director of the federal Bureau of Prisons. He seeks unspecified damages.

Justice John Paul Stevens asked whether the lawsuit against the lower-level officials could go forward, that Mueller and Ashcroft could be dismissed as defendants for now and added later if evidence turned up against them.

In the weeks after the Sept. 11 attacks, U.S. authorities detained 762 noncitizens, almost all Muslims or Arabs. Many of those held at the federal prison in Brooklyn suffered verbal and physical abuse, the U.S. Justice Department's inspector general found.

Justice Stephen Breyer said the U.S. government takes the position that those detained came from the same region of the world as the Sept. 11 hijackers and the detention policy was adopted with the purpose of preventing further attacks.

He questioned Reinert on whether the lawsuit should be allowed to drag on for years and take up the time of Ashcroft and Mueller.

Iqbal was arrested for having false Social Security papers. He pleaded guilty in 2002, was released in 2003 and deported to Pakistan. The lawsuit was filed in 2004.

The U.S. government paid $300,000 to settle with Iqbal's co-plaintiff and fellow detainee Ehab Elmaghraby, an Egyptian.

A Supreme Court ruling in the case is expected by June. (Editing by David Wiessler)

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