WASHINGTON (AP) — Efforts to avert a shutdown of the Federal Aviation Administration failed on Friday amid a disagreement over a $16.5 million cut in subsidies to 13 rural communities, meaning that at midnight nearly 4,000 people were to be temporarily out of work and federal airline ticket taxes suspended.

Lawmakers were unable to resolve a partisan dispute over an extension of the agency’s operating authority, which was to expire at midnight Friday.

The subsidy cut was included by Republicans in a House bill extending operating authority for the F.A.A., which has a $16 billion budget. Senate Democrats refused to accept the House bill with the cuts, and Republican senators refused to accept a Democratic bill without them. Lawmakers then adjourned for the weekend.

Underlying the dispute on rural air service subsidies was a standoff between the Republican-controlled House and the Democratic-controlled Senate over a provision in long-term funding legislation that would make it more difficult for airline and railroad workers to unionize.

Obama administration officials have said the shutdown will not affect air safety. Air traffic controllers will remain on the job. But airlines will lose the authority to collect about $200 million a week in ticket taxes that go into a trust fund for F.A.A. programs.

F.A.A. employees whose jobs are paid for with trust fund money will be furloughed, including nearly 1,000 workers at the agency’s headquarters in Washington, 647 workers at the F.A.A.’s technology and research center in Atlantic City and 124 workers at the agency’s training center in Oklahoma City.

Airline passengers could save money on their airfares, but the situation is complicated. Federal taxes on a $300 round-trip ticket are about $61, according to the Air Transport Association.

Airlines, alerted earlier this week that F.A.A. authority could expire, have been making adjustments to their computer systems and Web sites so that at midnight, taxes were to be no longer added to airfares, the association said.

One airline, US Airways, was already raising fares. Other airlines may try to reap a windfall profit from the tax holiday.

Passengers who bought their tickets before the shutdown, but who travel during the shutdown, may be due a refund, said Sandra Salstrom, a Treasury Department spokeswoman. That is because it is not clear whether the government can keep taxes for travel that takes place during a period when the government does not have authority to collect taxes, she said.

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