The government shutdown is over, but the federal courts’ financial woes persist.

The budget deal Congress approved on October 16 included $51 million in additional funding for the judiciary. But judges and federal public defenders warned the money won’t do much to relieve the financial pressure they’re already under.

“The federal defender system and the judiciary as a whole still needs money,” said Michael Nachmanoff, chief federal public defender for the Eastern District of Virginia. “I hope that Congress will appreciate the constitutional responsibilities of the court system and provide that money.”

The spending measure passed last week funds the government through January 15. It leaves in place most of the $350 million in cuts the judiciary made earlier this year. The additional appropriation bumped the judiciary’s budget up to $6.7 billion.

Chief Judge Ruben Castillo of the U.S. District Court for the Northern District of Illinois greeted the $51 million as good news. However, he said, it was unlikely to ease the pain of the ongoing cuts, known as sequestration. The budget deal was “far from a perfect ending,” he said, “but we’re pleased we’re operational at the least.”

For Castillo and judges across the country, continued cuts mean tough choices, from hiring freezes and cutting back on basic supplies and maintenance to furloughs. In the months leading to the shutdown, Senate and House committees passed proposals mostly restoring the judiciary’s funding to presequestration levels. Castillo said that gave him hope of future bipartisan agreement on fully funding the federal courts.

“I think a really precise evaluation needs to be made of the courts’ operations, rather than just saying, ‘Well, they’re like any other government agency,’ ” Castillo said. The constitutionally mandated element of the courts’ operations, he said, “ is what makes the courts unique.”

Of the additional $51 million approved last week for the judiciary, $26 million was designated for the defender services budget, which covers federal public defender offices and private lawyers appointed by the court to represent indigent criminal defendants. Public defenders endured furloughs and limits on resources to pay for experts, training and other expenses under sequestration. Private court-appointed lawyers haven’t been paid since mid-September and were bracing for more deferred payments and reduced hourly rates.The $26 million will be used to make payments to the private court-appointed lawyers, according to information provided to public defender offices by the Administrative Office of the U.S. Courts. The judiciary still expected to have to defer payments to those lawyers for up to two weeks in the 2014 fiscal year.

Nachmanoff said he lacks the lawyers, staff and other resources needed to handle cases. His office may avoid furloughs this year only because it already lost a number of employees due to the budget cuts. “It’s hard to be optimistic, but I am,” he said, pointing to the fact that Congress agreed on the extra $51 million. “You sound like an idiot to be too optimistic, given what we saw over the past six months, these last three weeks in particular,” he said.

The other $25 million Congress approved will go to the judiciary’s salaries and expenses budget. According to the admini­strative office, the money will give the judiciary a cushion to respond to budget needs.

The federal courts were spared the worst of the shutdown, which began after Congress failed to pass a budget by the start of the 2014 fiscal year on October 1. The courts found alternative sources of funding to temporarily keep courts fully operational. That money was expected to run out October 18.

Judges publicly expressed frustration with the budget stalemate. A growing number of chief judges — more than two dozen by the time lawmakers reached a deal — declared all employees essential under federal law, meaning they would keep working if the shutdown outlasted the judiciary’s funding.

Chief Judge Fred Biery of the U.S. District Court for the Western District of Texas was doubtful Congress would ever restore the $350 million in cuts. “It’s all tied up in politics,” he said. “We certainly hope they’ll restore a whole lot more, but I’ll believe it when I see it.”

Zoe Tillman can be contacted at Todd Ruger contributed.