As if one debate jeopardizing the function of the federal government wasn’t enough, another debacle playing out in Congress threatens to shut down the Federal Aviation Administration by Saturday.

This week, the stalemate over the debt ceiling has generated most of the headlines. Failure to raise it will force the government to make serious choices about how it will pay its creditors. It could even default on its debt.

But none of that will happen until Aug. 2. A much sooner date -- midnight Friday -- is the deadline by which Congress must settle its disputes about an FAA bill if it wants to avoid closing the agency and furloughing 4,000 employees. A shutdown would also temporarily halt airport construction projects funded by the FAA across the country, putting thousands of construction workers out of work, administration officials said.

“My message is this is no way to run the best aviation system in the world,” Transportation Secretary Ray LaHood said in a conference call with reporters Thursday afternoon.

Even if the FAA does shut down, airports would remain open, and air traffic controllers would continue to work and be paid, LaHood said.

The debate began when the Republican-controlled House passed an FAA authorization in April that included a provision that would make it more difficult for airline and railroad workers to unionize. The Democratic-controlled Senate, meanwhile, has approved a re-authorization that lacks those provisions.

As the deadline approached, lawmakers knew they needed to pass a stopgap bill to temporarily fund the agency while the dispute over the labor language was addressed. So last week, Republican Rep. John Mica introduced a bill that would fund the FAA through Sept. 16, which the House ultimately passed.

But that stopgap includes a controversial provision that would make cuts to a program that subsidizes the cost of air travel for flights at small airports. Under the program, the government pays airlines to serve airports they would otherwise avoid because the routes are unprofitable. The program has been a previous target of Republicans, who say it’s wasteful.

One of Mica’s proposals would have limited eligibility of the program called Essential Air Service to communities that are at least 90 miles from a medium or hub airport. Another includes a cap that would cut airports from the program that require subsidies of more than $1,000 per passenger. Mica, who has presented the changes as reasonable reforms, says a total of 13 airports would be cut from the program, saving about $16.6 million annually.

But among the airports that would say goodbye to the subsidies are facilities in the home states of powerful Democratic Senators, including Senate Majority Leader Harry Reid, Finance Committee Chairman Max Baucus and Commerce, Science & Transportation Committee Chairman Jay Rockefeller.

Democrats have said there’s no way they’ll pass the short-term extension, given the last-minute cuts by House Republicans. "Your attempt to punish the Senate by hurting small community air service has backfired -- this language only guarantees that the Senate will reject the FAA extension,” Rockefeller wrote in a letter to Mica.

So, as it stands, the future of the FAA remains in jeopardy.

The 4,000 soon-to-be furloughed FAA employees include engineers, scientists, planners and analysts, among other positions, who work across the country.

An even greater concern to localities is that, without an extension, the FAA’s Airport Improvement Program would have to temporarily close shop. As a result, $2.5 billion set aside for the program for the rest of the 2011 fiscal year couldn't be spent until a deal is made. Without authorization, construction at some airports would stop, and workers would be out of a job, LaHood said.

Additionally, without an extension, about $200 million a week in airline taxes cannot be collected and deposited into a special trust fund that funds some of the FAA’s work, according to the Department of Transportation.

This would mark the 21st temporary extension to the previous long-term FAA bill, which expired at the end of the 2007 fiscal year. LaHood is urging Congress to pass a “clean” bill absent the EAS reforms included by the House, which he blamed for the stalemate. “Congress has found the will on 20 different occasions, with rather short notice by the way, to pass a clean bill,” LaHood said. This time, he said, should be no different.

Republicans, unsurprisingly, have framed the issue differently, arguing that Senate Democrats would rather close the FAA than agree to a deal that cuts wasteful spending. EAS critics note that the program often subsidizes airports that are just a few hours' drive from larger hubs and suggest the program is really designed to ensure members of Congress from rural areas can have an easier time flying home.