The major budget cuts to the federal courts are here to stay—at least for this fiscal year.

Congress agreed late on March 22 to fund the government through September, heading off a threat of a government shutdown when existing budget authority expires later this week. But the legislation restored only a small slice of the $350 million in automatic cuts that hit the nation’s courts earlier this month.

The funding fight on Capitol Hill was one of the last opportunities until October 1 for Congress to undo mandatory government-wide cuts as part of a budget strategy called sequestration. Top court officials said that those cuts are unsustainable in the long run, and already pose problems like lengthy case delays, inadequate counsel for criminal defendants and reduced safety at courthouses.

The federal public defender services program, which court budget officials said was particularly hard hit because there are few areas to cut other than personnel and overhead expenses, got $9 million in cuts restored in the funding bill. However, that means defender services still will receive $43 million less during 2013.

Judge Thomas Hogan, director of the Administrative Office of the U.S. Courts, told Congress said that those cuts "could compromise the integrity of the defender function."

As part of the plan to deal with the broader cuts, administrators had decided to reduce allocations for defender salaries by 4 percent, non-salary funds by 25 percent and training funds by 50 percent. Payment of Criminal Justice Act panel attorney vouchers could be deferred for almost three weeks at the end of the fiscal year.

Hogan declined comment through a spokesman.

On Capitol Hill, the fight for court funds now turns to the 2014 budget, which takes effect on October 1. Judge Julia Gibbons of the U.S. Court of Appeals for the Sixth Circuit, chairwoman of the judicial conference’s budget committee, testified on Capitol Hill on March 20 that "we have a deep concern about our ability to fulfill our constitutional mission." She asked Congress to restore funding levels to the federal courts’ 2014 budget, as well as provide a $180 million increase from the 2013 budget.

Representative Ander Crenshaw (R-Fla.), the chairman of the Financial Services and General Government Subcommittee of the House Appropriations Committee, said the budget atmosphere would make that "tough" to do.

The nation’s federal courts are slashing spending on things like court security and court staff salaries – and might even temporarily halt civil jury trials later this year – because of the federal budget cuts. The largest share of the sequestration cuts, $93 million, would come from salaries, as previously reported by The National Law Journal. Court officials in each district will have to decide whether to achieve the cuts by closing courts, furloughing employees or laying off workers. The judiciary has estimated that the cuts could mean that 2,000 employees could be laid off this year, or face furloughs for one day each pay period, which would be the equivalent of a 10 percent pay cut.

Contact Todd Ruger at truger@alm.com.