The federal judiciary never felt the full brunt of the 16-day government shutdown, since alternative funds allowed courtrooms and clerks’ offices to operate normally when other government operations stalled.

The deal that reopened the government Thursday, however, leaves in place most of the $350 million budget cuts to the judiciary made earlier this year—a situation that a top judiciary official this summer predicted would be “devastating for the federal courts.”

The last-minute deal to reopen the government did provide a relatively small bump of $51 million in annual appropriations for the federal courts and for public defenders, out of a $6.7 billion overall budget. Part of that, a $26 million increase for defender services, would primarily go to pay the backlog of attorney fees under the Criminal Justice Act, which funds court-appointed private counsel. It could also help alleviate some of the pressure on federal public defender offices around the country that were forced to put lawyers and staff on furlough at times this year.

The judiciary will now continue its unusually public push to convince Congress to fully undo the spending cuts that came as part of government-wide reductions called sequestration, said U.S. Circuit Judge Julia Gibbons, chairwoman of the budget committee of the U.S. Judicial Conference.

“Certainly we will continue the efforts that we’ve made over the last number of months and we’ll keep giving Congress our message about the need for adequate funding,” Gibbons, who serves on the U.S. Court of Appeals for the Sixth Circuit, said in a telephone interview Thursday.

The $51 million increase will help, Gibbons said, but it only provides the funding at that rate through January 15. “It is really just a first step toward repairing the damage that’s been occasioned and the harm that’s occasioned by the budget cuts over the last couple of years,” Gibbons said.

Even before the deal to end the shutdown, Gibbons and the federal courts had already announced plans to ask Congress for a “funding anomaly” if sequestration-level funding continued into the new fiscal year on October 1. An anomaly would give the judiciary extra money outside the normal budget process.

But the shutdown deal opened another, more promising avenue to press Congress for money. The House and Senate have appointed a conference committee of legislators to negotiate a budget resolution by December. The committee will focus, in part, on finding better spending cuts than the blunt, across-the-board slashes imposed by sequestration. The biggest hurdle will be finding common ground between the House and Senate budget plans.

One thing Congress appears to agree on: More money for judiciary. This fall, appropriations committees in both houses of Congress approved budgets that would, at a minimum, roughly restore money to the judiciary to pre-sequestration levels.

Gibbons said those appropriation bills and the $51 million in the shutdown deal shows Congress understands the courts are vital to the proper functioning of democracy, good stewards of taxpayer dollars and are hurt by budget cuts.

“I take it as a sign of congressional recognition of all those things,” she said.

There are scarce resources and many demands, however, and Republicans remain intent on cutting government spending. Senator Jeff Sessions (R-Ala.), the top Republican on the Senate Budget Committee and a member of the Senate Judiciary Committee, said following Wednesday’s vote that this would be the lowest funding year the courts would have under the sequestration.

“I’m not sure there’s as big a crisis as some would say,” said Sessions, who will be a leading figure on the conference committee.

Sessions said he was convinced that public defenders were being hurt. “This will be more money going to them but it will be paid for by a reduction in spending somewhere else, so it doesn’t violate the budget limits for spending,” Sessions said.

The Constitution Project, a bipartisan legal watchdog group, said Thursday that the $26 million for defender services would not restore adequate staffing or prevent further furloughs in many offices across the country.

“While we are grateful budget negotiators recognized the need to stop the bleeding in the public defenders offices, Congress will need to provide much higher levels of funding when they pass a budget if they want to allow federal defenders to carry out their constitutionally required duties,” Virginia Sloan, president of The Constitution Project, said in a written statement.

It was not immediately clear how the $51 million bump got into the legislation to reopen the government. Following the vote, Senator Sheldon Whitehouse (D-R.I.), a Judiciary Committee member, said he had not known that the money was included in the bill, which had been in final form for a only few hours before the vote.

“But I’m delighted that’s the case,” Whitehouse said. “We had hearings on this in judiciary, and our system of justice is a model of the world, and to leave it underfunded and unable to execute the way it should is really kind of a national shame.”

Sessions, when asked how the money was put in the bill, said: “Well, I’m not sure.” Senator Patrick Leahy (D-Vt.), the Judiciary chairman who presided over the Senate during the vote, did not answer directly when asked about the money.

“The federal courts are actually the best courts in this country. We’d like to keep our courts working,” Leahy said in a hallway outside the Senate floor. He added before boarding an elevator: “I only preside.”

A spokesman for Senator Dianne Feinstein (D-Calif.), a veteran Judiciary member and a key negotiator Appropriations member, said she did not insert the money. A spokesman for Senator Christopher Coons (D-Del.), chairman of the subcommittee on bankruptcy and the courts, said that he could not get into the specifics.

Senator Richard Blumenthal (D-Conn.) said he had heard about the matter before the vote, and that he believes the budget conference should restore the judiciary’s funding at least back to pre-sequestration levels.

Gibbons, who serves on the U.S. Court of Appeals for the Sixth Circuit, in July laid out for the Senate the consequences of leaving “a hard freeze” for FY 2014 at existing sequestration levels. “Such a scenario would be devastating for the federal courts,” she wrote.

Clerks of court and probation and pretrial services offices could be forced to lay off 1,800 employees through the end of the budget year in September 2014, creating a backlog in the processing of civil and bankruptcy cases and a reduction in the hours that clerks’ offices are open to the public, Gibbons said.

There would be a $45 million shortfall in the court security account, forcing difficult cuts for court security officers and the Federal Protective Service. Such cuts have the potential to put judges, court personnel, and the public who enter courthouses at serious risk, she warned.

“For example, courthouses that currently have security coverage 24 hours a day, seven days a week, would have services reduced overnight and on the weekends. This includes many courthouses in large metropolitan cities, several of which regularly handle terrorism cases,” Gibbons said in written testimony for the Senate Judiciary Committee.

Nothing has substantially changed in those assessments since then, Gibbons said.

The Judicial Conference announced in August that Criminal Justice Act attorneys, appointed by the court to represent indigent defendants, would absorb a $15 cut in hourly rates. That move was meant to spare additional cuts from federal public defender offices.

Gibbons said it is too early to say how the judiciary will spend the other $25 million included in Thursday’s shutdown deal. “There are so many needs within the judiciary and it’s going to take a few days to assess the best utilization of the money,” she said.

All of these measures would come on top of layoffs and cost-cutting because of years of flat funding for the judiciary.

The courts have been sounding the alarm for almost a year. In May, Gibbons and Judge Thomas Hogan, then-director of the Administrative Office of the U.S. Courts, asked Congress for a $73 million emergency supplemental appropriations request to help ease sequestration cuts.

The request included $41 million for defender services, in part to avoid furloughs and staffing losses in federal defender organizations during the fourth quarter of FY 2013.

In August, the chief judges of nearly every federal district court joined in a four-page letter to warn Congress of the damage budget cuts already had done to judicial operations. The letter was an unusual public display of agreement and lobbying, and described weakened courthouse security, reduced public safety because of probation and parole cuts, and caused dire problems for federal public defender offices. Congress has not acted on the emergency request.

Contact Todd Ruger at truger@alm.com.