The Federal Aviation Administration was alarmed.
The Defense Department had passed along new laser technology to border officials who were planning to use it to interdict drones crossing into the United States from Mexico. But F.A.A. officials were concerned about the potential hazards of using lasers near the airspace where commercial planes were landing at El Paso International Airport, and wanted more information.
After border officials went ahead and used the technology, ignoring the pleas, the F.A.A. determined it had no further leverage to use. So it played its only card — or perhaps overplayed it.
Late Tuesday night, it abruptly closed El Paso’s airspace, an extraordinary measure that disrupted travel and shocked local residents.
It was the latest dust-up in an increasingly fractious relationship between two powerful government agencies, the F.A.A. and the Defense Department, as they attempt to fulfill differing objectives in a chaotic administration.
The F.A.A. is responsible for the safety of the national airspace and the more than three million people who travel through it every day. The Defense Department is tasked with keeping the United States safe, at home and abroad.
Those twin goals collided this week in an embarrassing spectacle, after the F.A.A., frustrated by its inability to obtain its desired safety briefing on the new anti-drone laser technology, announced a 10-day shutdown of the airspace for a city of nearly 700,000 people.
Officials there felt the military had not provided them with the information they needed to ensure that airplanes could maneuver safely through the skies while the technology was being tested, according to three people who spoke on the condition of anonymity because they were not authorized to discuss the decisions.
Defense Secretary Pete Hegseth lent the technology to Customs and Border Protection personnel, because the agency had wider legal authorities inside the United States to use such tools, said two U.S. officials who requested anonymity to talk about operational matters.
But the episode turned bizarre when C.B.P. officials used the technology on what they thought was a cartel drone earlier this week but appeared to have been a party balloon, according to two officials. Defense Department officials were present at the incident.
On Wednesday morning, as passengers, airport workers and municipal officials in El Paso fumed over the closure, the White House quickly engineered a course reversal, resulting in the F.A.A.’s cancellation of the shutdown after about seven and a half hours.
Normalcy had resumed, at least for air travel. But at the Pentagon and at F.A.A. headquarters in Washington, much was unresolved.
“There’s no excuse as to why agencies can’t work together when you’re making decisions like changing airspace rules or shutting down airspace,” said Jeff Guzzetti, an aviation safety expert and former accident investigator.
“It appears that they’re siloed,” he added of the F.A.A. and Pentagon. “Typically people would overcome their silos. They would come together for things like airspace design and cooperation. But that doesn’t appear to be the case recently, and I don’t know why.”
The Pentagon did not address repeated questions about the anti-drone technology. Hannah Walden, the F.A.A.’s assistant administrator for communications, did not respond to a request for comment.
Sean Duffy, the transportation secretary, has been mum on the topic since Wednesday, when he asserted that the shutdown was caused by a military response to a Mexican drone incursion.
On Thursday, several people who had been briefed on the incident said it was unclear whether the safety briefings the F.A.A. had requested from the Defense Department had occurred since the closure was lifted — or whether a moratorium on the use of the anti-drone technology was in place until those briefings could be held.
Transportation safety officials have been tussling with the Pentagon since Jan. 29, 2025, when an Army Black Hawk helicopter flying a training mission near Ronald Reagan National Airport crashed into an American Airlines flight that was en route to land there, killing 67 people.
The accident, which government officials have attributed to a variety of factors, including the Army crew’s inability to properly use a safety practice involving seeing and avoiding other aircraft, was the deadliest aviation disaster on U.S. soil in 24 years.
In early May last year, three months after the accident occurred, the Army resumed the same type of training flights that the fallen crew had been conducting. Almost immediately, there was a problem: a series of communications issues led another Army Black Hawk that was attempting to land near the Pentagon to fly uncomfortably close to two commercial airplanes headed for National Airport. Both airplanes aborted their landings.
Mr. Duffy was furious. In a May 2, 2025, post on X, he castigated the Pentagon.
“Unacceptable,” he wrote. “Our helicopter restrictions around DCA are crystal clear,” he added, using an abbreviation for National Airport. “I’ll be talking to the @DeptofDefense to ask why the hell our rules were disregarded.”
Days later, he criticized the Pentagon for falling short of its promises of “radical transparency” on its Washington helicopter operations.
The Pentagon did not respond publicly to Mr. Duffy’s broadsides, which he soon walked back. But additional tensions followed.
A government investigation into the causes of the January accident handled by the National Transportation Safety Board drew attention to the Army’s practice of flying through Washington’s airspace without broadcasting its position to other pilots, as most other airspace users were required to do. The Army had sought, and received, permission to fly without broadcasting technology, even on training flights, by arguing that its operations had to be kept confidential to maintain national security.
Some lawmakers cried foul over those exceptions, arguing that using the technology could have helped prevent the accident. Their case gained renewed attention in December, when Congress considered — and ultimately passed — an annual defense bill that effectively rolled back restrictions on when military aircraft could turn off the broadcasting technology.
Days later, when a JetBlue passenger plane flying over the Caribbean came less than 20 seconds from colliding with an Air Force refueling plane that was flying without using broadcasting technology, the stakes of such disputes were thrown into sharp relief again.
“It’s outrageous,” the JetBlue pilot told an air traffic controller, according to audio recordings of the flight communications. “We almost had a midair collision up here.”
Both the Defense Department and the Department of Homeland Security share responsibility for securing the nation’s southern border, but their remits are different.
The Pentagon is authorized to detect, track and, if necessary, disable or destroy drones that threaten certain military installations in defined airspace around those sites.
The Department of Homeland Security has similar anti-drone authorities, but they are related to nonmilitary venues, such as certain federal buildings, prisons and other domestic security sites. The department also focuses on protecting large events, like the Super Bowl.
Kate Kelly covers money, policy and influence for The Times.
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