After staying afloat on the same budget for two years in a row, legislative branch agencies have begun a third year with no increases for new programs, new hires or even, in some cases, simple inflation.

A late federal appropriations process is nothing new. But it threatens to temporarily freeze the plans of agencies such as the Government Accountability Office and the Office of Compliance, jeopardizing annual salary raises in one and delaying an inspection of the Capitol Visitor Center for the other.

“There’s only one express annual responsibility for Congress under the Constitution and that’s to pass appropriations bills, and yet with recurring frequency that hasn’t gotten done in a timely manner,” said Comptroller General David Walker, who heads the GAO. “The system is broken, and it needs to be fixed.”

The legislative agencies have been in funding suspension since October 2006, with Congress passing several continuing resolutions throughout the year. Now lawmakers have passed another CR, keeping the government running on last year’s funding level until Nov. 16.

For more federal entities, that means year three of the same — or at least similar — budgets.

“The six-week CR will be manageable. The real challenge is if the CR goes beyond three months,” Walker said, adding that about 80 percent of the GAO’s budget goes toward compensation for employees. “If it goes beyond three months, we will have serious issues that will need to be addressed.”

Like Walker, several agency officials say they can handle a six-week CR, postponing new programs and new initiatives until the new budget is passed. But some worry that their appropriations bill will get lost in the shuffle, delaying it even longer.

In fact, the legislative branch appropriations bill is often pushed to the back of the line, said Stephanie Allen, spokeswoman for Sen. Mary Landrieu. The Louisiana Democrat chairs the Appropriations Subcommittee on the Legislative Branch, which passed its spending bill in June.

“Given that it’s the bill that funds Congress, it is obviously very important, but when Congress is dealing with homeland security, that’s usually done prior to the legislative branch,” Allen said, adding that the CR also is no surprise. “The Legislative Branch Subcommittee has been working with agencies to make sure they know what’s up. This is sort of par for the course.”

Expected or not, the delay still forces agencies to run bare-bones operations. In the Office of Compliance, the delay will stall several new safety and health initiatives, including a comprehensive inspection of the Capitol Visitor Center, said Beth Hughes-Brown, the OOC chief financial officer. The OOC also is hoping to hire experts to oversee the repair of Capitol Power Plant tunnels after an inspection found asbestos, heat and structural violations. And, she said, the agency needs four new positions, including a safety and health compliance officer.

But Hughes-Brown said the agency was prepared for the delay.

“I don’t want to say we’re used to it, but it is a reality,” she said. “Our legislative subcommittees treat us well. They did prepare us for this possibility.”

Spokesmen for the Government Printing Office and Library of Congress said the CR will make things tight, but they declined to go into specifics. For the interim, some new programs will have to be stalled, but the CR “would not impose an onerous hardship on the Library,” LOC spokesman Matt Raymond said.

The Library pleaded with lawmakers to increase their fiscal 2008 budget this summer, arguing that programs might have to be cut if more money wasn’t given. For the moment, both the Senate and the House bills allocate about $577 million for the agency, out of the $661 million requested. But the bill hasn’t made it to the Senate floor, and there’s no indication of when it will. Until a conference is held on the bill, it’s uncertain what any of the legislative branch agencies will get.

The GPO is hoping for a quick resolution, said its spokesman, Gary Somerset.

“Yes, the budget is tight. If GPO continues to operate under a CR, it will become more difficult to meet the obligations required by Congress and the American public,” he wrote in an e-mail. But “GPO is optimistic that Congress will pass an appropriation bill soon.”

Walker said the main problem is that agencies are left wondering whether the House or Senate budget will come out on top.

For the GAO, there’s a difference of $7 million between the two bills, with the House approving a $503 million budget and the Senate considering a $510 million appropriation. Either is more than the agency enjoyed in recent years: the fiscal 2007 budget was about $489 million. However, the GAO needs at least $510 million to keep up with an ever- increasing workload, Walker said. Congress lays more and more responsibilities on the agency, he said, but it doesn’t tie those added burdens to a larger budget.

“The real question is what’s our final appropriation going to be and when are we going to get it,” Walker said.