Sequestration budget cuts could stand between Osama bin Laden's son-in-law, Suleiman Abu Gaith, and a trial on American soil timed almost to match up with the anniversary of the September 11 attacks.

Judge Lewis Kaplan today said Abu Gaith could go on trial in federal court in Manhattan as early as September of this year, around the anniversary of the 9/11 attacks the suspect lauded in al-Qaeda videos. Gaith's lawyer protested, saying a September start might be too soon, because of sequester cuts to public defenders.

The judge said it would be unfortunate if sequestration issues interfered with a trial of this importance, and he agreed to appoint other lawyers to assist the federal defenders service.

The U.S. court system stands to lose almost $350 million to sequester cuts. Last month Judge Julia Gibbons, chair of the Judicial Conference Budget Committee, testified that leaving sequestration as is would "have a devastating effect on federal court operations nationwide."

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"We believe we have done all we can to minimize the impacts of sequestration but a cut of this magnitude, particularly so late in the fiscal year, will affect every facet of court operations and impact the general public as well as individuals and businesses looking for relief in the courts," Gibbons told the House subcommittee on financial services and general government of the appropriations committee.

She warned the courts could face up to 2,000 layoffs or furloughs before September.

"In our defender services program, federal defender attorney staffing levels will decline which could result in delays in appointing defense counsel for defendants," Gibbons said.

Last week, the results of furloughs became visible as a federal public defenders' office in Maryland all but shut down, while elsewhere, some agencies have managed to delay staffing cuts until mid-April or later.

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Republicans have criticized the president for his administration's decision to try Abu Gaith in a federal court, instead of a military tribunal at Guantanamo Bay.

ABC's Aaron Katersky and Ariane de Vogue contributed to this report.