Congressional leaders reached agreement Thursday on temporary funding for the Federal Aviation Administration, ending a stalemate that cost 4,000 furloughed federal workers almost two weeks of pay and shortchanged the Treasury of more than $300 million.

“This agreement does not resolve the important differences that still remain,” Senate Majority Leader Harry M. Reid (D-Nev.) said Thursday afternoon. “But I believe we should keep Americans working while Congress settles its differences, and this agreement will do exactly that.”

It was uncertain whether Congress would act to restore back pay to the furloughed FAA employees. Tens of thousands of construction workers who have been laid off since July 23 seemed unlikely to recoup their lost wages.

Mike MacDonald, regional vice president of an FAA union, said he was not focused on whether furloughed workers would receive back pay. “We’re just really glad we’re getting back to work,” he said.

The agreement came about after Congress was taken to task for heading off for summer vacation while thousands of workers were faced with weeks without pay. Four days after what they described as “bullying” by House Republicans, Senate Democrats gave in and accepted the House extension to which they had so vociferously objected.

“House Republicans made it clear they would continue to hold the entire aviation system hostage,” said Senate Commerce Chairman John D. Rockefeller IV (D-W.Va.), who leveled the bullying charge on the Senate floor. “I deplore those tactics, but ultimately the stakes for real people are too high.”

During the stalemate, the FAA was unable to collect as much as $30 million a day in ticket taxes after its congressional authorization expired.

The Senate is expected to meet Friday and approve by unanimous consent the House extension of FAA funding.

House Transportation Committee Chairman John L. Mica (R-Fla.), who had led the charge for Republicans, could not be reached Thursday to comment.

The agreement promises a temporary truce but far less than a settlement of the disputes that have left the FAA without a long-term funding authorization for almost four years. Unless House and Senate negotiators are able to reach agreement on a new funding package within six weeks, they will face the prospect of extending current funding levels for the 22nd time.

All but a handful of the more than 250 differences between the House and Senate bills are said to have been resolved, but the last few are notably thorny.

Foremost among them is disagreement over a rule that governs efforts to unionize airline workers. The House bill seeks to revert to an earlier, longtime standard under which those who do not cast ballots in a union organizing effort are counted as voting no.

Senate Democrats are dead set against that change.

“It’s clear the right wing of the GOP wants to undo worker protections and may again block progress on the FAA bill in September in order to get its way,” Rockefeller said.

Transportation Secretary Ray LaHood, who worked behind the scenes and rallied public support to end the impasse, called the agreement a “tremendous victory for American workers everywhere.”

“From construction workers to our FAA employees, they will have the security of knowing they are going to go back to work and get a paycheck, and that’s what we’ve been fighting for,” LaHood added. “We have the best aviation system in the world, and we intend to keep it that way.”

The battleground that caused the partial shutdown of the agency was over a bill to extend funding until September. All but one of the 20 previous extensions had continued funding at the current level.

Last week, Mica said Republicans were frustrated with the tempo of negotiations to resolve differences in the long-term bills. He said he feared that the Senate was willing to continue the extensions rather than tackle issues in the larger bill.

Mica said he tacked onto the 21st extension bill provisions he knew would antagonize key senators as a means of pushing them toward meaningful negotiation.

Antagonize them, he did, with senators furious that a routine extension bill now carried provisions that would cut subsidized air service to three small airports, one in Reid’s home state and another in that of Senate Finance Committee Chairman Max Baucus (D-Mont.).

After agreement was reached, Senate Democrats expressed hope that LaHood might grant waivers to allow the subsidies to continue.

Senators also pointed out that although both houses passed the long-term reauthorization bills in the spring, the House had yet to appoint conference committee members, leaving the task of resolving differences primarily to staff members.

Staff writer Lisa Rein contributed to this report.