The Federal Aviation Administration (FAA) partially shut down Saturday, as Congress failed to reauthorize the agency's funding.

“I’m very disappointed that Congress adjourned today without passing a clean extension of the FAA bill," Transportation Secretary Ray LaHood said in a Friday statement. “Because of their inaction, states and airports won’t be able to work on their construction projects, and too many people will have to go without a paycheck. This is no way to run the best aviation system in the world.”

About 4,000 FAA employees are now furloughed without pay, according to the FAA, as the Senate on Friday failed to approve a controversial House-passed extension of taxes that help fund the FAA.

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“The FAA employees who will be furloughed perform critical work for our nation’s aviation system and our economy,” FAA Administrator Randy Babbitt said in a statement. “These are real people with families who do not deserve to be put out of work during these tough economic times.”

LaHood has stressed that essential personnel related to airport and air safety would not be cut. "I want to reassure the flying public that, during this period, safety will not be compromised," he said earlier.

The Republican-controlled House and the Democrat-controlled Senate are blaming each other for failing to pass an FAA reauthorization.

“It is unbelievable that after the House passed the 21st FAA extension, the Senate departed Washington and left the FAA and many of its employees behind,” House Transportation and Infrastructure Committee Chairman John Mica (R-Fla.) said. “In light of the nation’s pending financial disaster and soaring deficits, they couldn’t find a way to cut even a few million dollars by accepting this minor request to reduce outlandish subsidies.”

But Senate Commerce, Science and Transportation Committee Chairman Jay Rockefeller John (Jay) Davison RockefellerBottom Line World Health Day: It's time to fight preventable disease Lobbying World MORE (D-W.Va.) accused House Republicans of playing politics with the bill.

“The refusal by the House to extend FAA’s funding authorities is a disservice to the American public and the aviation industry," Rockefeller said. "I am disappointed and stunned by their failure. We had negotiated in good faith for four months, but when senior members of the House leadership admitted that they would try to gain political ‘leverage’ over the Senate, they effectively turned the aviation system into a political prop."

The House on Wednesday approved an extension of FAA taxes until Sept. 16, but that extension included language that would prohibit federal subsidies from going to three small airports in Montana, Nevada and New Mexico because tickets there are subsidized at more than $1,000 per ticket.

The House extension included language eliminating subsidies to 10 small airports because they are within 90 miles of a medium or large airport. However, this language is also in a Senate-passed bill.