CHALK UP ANOTHER victim of partisan politics in Congress: the Federal Aviation Administration. The agency’s last long-term authorization lapsed four years ago. Earlier this year, the Republican-majority House and Democratic-majority Senate each passed new long-term bills to replace a series of short-term funding extensions that kept the agency operating in the interim. But they have been unable to resolve major differences between the two bills, and the last extension expired on Friday. Consequently, the FAA has had to furlough thousands of employees around the country and suspend airport modernization projects worth $2.5 billion.

The partial shutdown doesn’t affect air traffic control, so the flying public won’t feel much immediate impact. But the airlines are no longer collecting millions of dollars in federal excise taxes, which could force the government to try to collect it from them when the FAA’s legal authority is reinstated.

What’s at issue? A key dispute relates to Essential Air Service (EAS), a federal program that subsidizes airports in rural America. Enacted in 1978 to maintain flights to remote locations that would otherwise have lost them because of airline deregulation, the program expanded well beyond that original purpose as Congress spotted its pork-barrel potential.

Between 1997 and 2007, spending quadrupled from $25.9 million to $109.4 million, and the number of destinations increased from 95 to 145 — about a fifth of all commercial airports in the country. Quite a few airports subsidized by EAS are within 100 miles of larger airports, according to the Government Accountability Office. EAS flights operated at 37 percent of capacity in 2008, and the federal government pays a median subsidy of about $100 per passenger.

The House FAA reauthorization bill would have phased EAS out by 2014, except for Alaska and Hawaii. The Senate version, however, would have funded it at the current level of $200 million per year, with an amendment ending service only to a few especially heavily subsidized locations. The Senate’s approach may have something to do with the fact that the bill’s author, Democrat John D. Rockefeller III, hails from West Virginia, which has a number of small airports.

Accusing the Senate of dragging its feet, House Transportation Committee Chairman John L. Mica (R-Fla.) put a $16.5 million EAS cut into the latest House version of the FAA extension, which Mr. Rockefeller rejected. Democratic senators, echoed by the Obama administration, accuse Mr. Mica of violating a long-standing practice of not adding policy changes to FAA extensions. Mr. Mica says he was merely adding a version of the cost-shaving amendment the Senate had already accepted.

And here we are. A prolonged halt to needed airport modernization is not in the country’s interest. But neither is the notoriously wasteful EAS, which was singled out earlier this year in the GAO’s 345-page report on federal “duplication, overlap and fragmentation.” Whatever else they decide to do about the nation’s air transportation system, members of Congress from both parties should make it their business to reform that program.