An air traffic controller works at Newark Liberty International Airport in New Jersey in May 2015. (Julio Cortez/Associated Press)

The Senate on Thursday ignored President Trump’s desire to lop more than 30,000 workers from the federal payroll, approving legislation that protects the Federal Aviation Administration from being split in two.

Trump endorsed with great fanfare this month a House plan to spin off air traffic controllers and close to 20,000 other workers into a nonprofit private corporation. Flanked by several former secretaries of transportation at a White House ceremony, Trump said: “The previous administration spent over $7 billion trying to upgrade the system and totally failed. Honestly, they didn’t know what the hell they were doing, a total waste of money.”

But an increasingly independent Senate, emboldened by Trump’s legislative failures, opted to disregard the White House push to privatize the controllers and those working on modernizing the aviation system.

“I remain open to moving the FAA’s functions into a not-for-profit nongovernment body, but I also appreciate that sincerely held concerns exist,” Sen. John Thune (R-S.D.), chairman of the Senate Commerce Committee, said Thursday as his committee approved a bill that would keep the FAA intact. “I hope and expect that we will consider this proposal more fully as the bill advances.”

Sen. John Thune (R-S.D.) speaks during a weekly news conference after a policy luncheon on Capitol Hill on June 13. (Zach Gibson/Getty Images)

The committee’s ranking Democrat, Sen. Bill Nelson (Fla.), was blunter: “The support is not there on this committee or in the Senate.”

In talking with reporters last week, Thune acknowledged the lack of committee support, adding, “If that issue were to get addressed, it would probably have to be on the [Senate] floor or in conference.”

The bipartisan Thune-Nelson bill requires greater accountability by the FAA on the much-criticized pace of the modernization program known as NextGen. It also includes new protections for airline passengers, deals with safety and privacy issues in the use of drones, and increases airport funding.

Airlines would be required to refund services, such as early boarding and seat assignments, that the passengers do not ultimately receive. Addressing another passenger complaint — shrinking seat sizes — the bill asks the FAA to review the safety implications of seat size.

With Congress facing a Sept. 30 deadline to approve FAA funding authorization, the privatization proposal is a big hurdle in an otherwise bipartisan agreement.

The House Transportation Committee on Tuesday approved an authorization bill that would create the nonprofit private corporation.

At issue is the FAA’s handling of the $36 billion NextGen program. Often described as a “GPS-based system,” it is a far more complicated system that would move U.S. aviation into the 21st century. But Congress has grown increasingly frustrated with the FAA’s progress amid regular critical reports from oversight agencies.

Critics of the privatization plan argue that the corporation’s board would come to be dominated by the airlines, and they fear that this domination would come at the expense of those who operate small planes and corporate jets. More significantly, they worry that airline dominance would diminish service to smaller airports and those in remote, rural areas.

The proposal to break off more than half of the FAA’s workforce has divided the two unions that represent most of the workers

“Severing air traffic control from the federal government is an unnecessary undertaking for a system that is not broken,” Mike Perrone, president of the 11,000-member Professional Aviation Safety Specialists union, said in a statement Wednesday. “We believe that our national airspace system is a complex entity that works for all users of the system today because of its public structure and accountability to Congress and the American people.”

That position is counterbalanced by the National Air Traffic Controllers Association (NATCA), which has almost 20,000 members and supports the House bill.

“After extremely careful review, consideration and deliberation, we have decided to support the bill because it fully aligns with NATCA’s policies, practices and core principles,” said NATCA President Paul Rinaldi. “This bill protects our workforce — including pay, benefits, retirement and collective bargaining rights.”