The Pentagon, CBP and the FAA said in a statement that the military mitigated "a seemingly threatening unmanned aerial system operating within military airspace."

The U.S. government said it would do better to communicate between agencies after the military used a laser to shoot down a Customs and Border Protection drone in Texas on Thursday.

U.S. Customs and Border Protection flew a drone into military airspace near Fort Hancock, Texas, without notifying anyone, and the U.S. military in turn took down the drone using a high-energy laser, a U.S. official told NBC News Friday.

After the drone was assessed, the military determined it belonged to CBP, the official said. The Pentagon said proper protocols were followed before the laser system was used.

Some Democratic members of Congress, including the ranking members of the House Homeland Security and Transportation committees, called the incident another example of “incompetence.”

It comes two weeks after CBP used a military laser to shoot down what turned out to be party balloons in Texas, which caused the temporary closure of El Paso’s airspace.

The Pentagon, CBP and the Federal Aviation Administration acknowledged the latest incident in a joint statement Thursday. They said there were no commercial aircraft in the vicinity.

“At President Trump’s direction, the Department of War, FAA, and Customs and Border Patrol are working together in an unprecedented fashion to mitigate drone threats by Mexican cartels and foreign terrorist organizations at the U.S.-Mexico Border,” the agencies said in the statement, using the rebranded name of the Department of Defense.

“This reported engagement occurred when the Department of War employed counter-unmanned aircraft system authorities to mitigate a seemingly threatening unmanned aerial system operating within military airspace,” they said.

“These agencies will continue to work on increased cooperation and communication to prevent such incidents in the future,” the agencies said in joint statement.

The statement did not specify that a CBP drone was hit.

Rep. Bennie Thompson, D-Miss., the ranking member on the House Homeland Security Committee, along with the Democratic ranking members on the House Transportation Committee and the ranking member of the Aviation Subcommittee, criticized the reported mishap but had not been briefed on it.

“Our heads are exploding over the news that DoD reportedly shot down a Customs and Border Protection drone using a high risk counter-unmanned aircraft system,” they said in a joint statement.

They also criticized the Trump administration for “sidestepping” a bipartisan bill to train drone operators and improve communication among the Pentagon, FAA and Department of Homeland Security.

“Now, we’re seeing the result of its incompetence,” they said.

The earlier laser firing was done by the CBP near Fort Bliss, about 50 miles northwest, and prompted the FAA to shut down air traffic at El Paso airport and the surrounding area. This time, the closure was smaller and commercial flights were not affected.

The FAA said earlier Thursday that it had expanded the airspace closure around Fort Hancock.

The El Paso shutdown two weeks ago lasted only a few hours but it raised alarm and led to a number of flight cancellations in the city of nearly 700,000 people not far from the Mexican border.

NBC News previously reported that the closure came after CBP officials used an anti-drone laser that was provided by the military to shoot down what was later identified as party balloons, according to four people familiar with the matter.

The CBP did so without coordinating with the FAA, the four people said, and the FAA shut down the airspace.

Afterward, members of Congress said it appeared to be another example of dysfunction within the government with different agencies failing to coordinate with each other.

Transportation Secretary Sean Duffy said he was planning to brief members of Congress sometime this week about what happened. He said at an unrelated news conference last Friday that it wasn’t a mistake for the FAA to close the airspace in El Paso and that he doesn’t think it was a communication issue that led to the problems.

Sen. Tammy Duckworth, the ranking member on the Senate’s Aviation Subcommittee, said the situation Thursday was alarming and demanded independent investigations.

“The Trump administration’s incompetence continues to cause chaos in our skies,” she said.

Duckworth, D-Ill., said that the Defense Department reportedly used a “high energy laser” to shoot down the drone.

The investigation into last year’s midair collision near Washington, D.C., between an airliner and an Army helicopter that killed 67 people highlighted how the FAA and the Pentagon were not always working well together.

The National Transportation Safety Board said the FAA and the Army did not share safety data with each other about the alarming number of close calls around Reagan National Airport and failed to address the risks. (NBC news)