As Washington has become increasingly partisan and year-long budget agreements harder to come by, Congress has relied more and more on stopgap budgets. Today, the House is scheduled to pass one funding the government for the next six weeks. Such fixes let Congress dodge the big budgetary questions, but they come at a cost. Even when there isn’t a government shutdown, the growing reliance on continuing resolutions has resulted in government waste and lost productivity for scores of government agencies.

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Congress has slowly begun to realize how serious these unintended consequences are. After the GAO’s report came out, legislators realized that it wasn’t looking good to let budget deadlocks hamper health care for veterans. They decided to make an exception for the Veteran Health Administration, giving the agency “advance appropriations” that would fast-track their money for the year. The Corporation for Public Broadcasting also receives that exception. But the vast majority of other agencies haven’t been so lucky.

When there’s only a short-term extension, an agency’s budget for the forthcoming year is put on hold. There’s often a moratorium placed on new projects — and when the next year’s budget finally does come in, there’s a rush to either spend money or cut back in ways that weren’t anticipated to meet the fiscal year’s targets. Still, government workers are required to write up full-year budgets, only to see Congress throw them out the window. “There is the constant talk of government waste, and wasting taxpayer dollars all the time. But in every agency, there are people like me who spend three to four months a year working on appropriations,” a policy analyst for a health-related agency tells me. “That’s three months of the year that could have been spent doing something more productive.” The additional hours managing Congress’s foot-dragging add up: The FBI estimated that managing 2009’s CR cost the agency extra 600 hours of labor, according to the GAO study.

And it’s not only government workers who are forced to pick up Congress’s slack: Stopgap budgets can also have a direct impact on Americans who receive government services, the GAO explains. The Food and Drug Administration, for example, told the GAO that CRs cause delays in hiring and training staff, which have made it difficult for the agency to conduct its targeted number of food and medical device inspections — a potential risk to public safety. The Federal Bureau of Prisons says delayed hires make it hard to keep up the ratio of prisons officials to inmates as prisons populations rise.

So even when there isn’t a government shutdown, there’s still a practical impact on the taxpaying public — in terms of wasted money and reduced services — when Congress keeps resorting to stopgap solutions. That’s all that may be politically possible in a divided, deadlocked Congress, and it’s certainly preferable to the alternative. But it also comes with real costs.