Democratic members of Congress have expressed astonishment and anger at what they claim is the incompetence of the Trump administration after the US military used a laser on Thursday to shoot down what it thought was a threatening drone on the US-Mexico border in Texas but later turned out to belong to US Customs and Border Protection (CBP).

The apparent confusion between two entities in the US government led to airspace being closed around Fort Hancock, right along the border. It was the second time in two weeks that air traffic was disrupted in the region as a result of a high-energy laser being deployed against drones.

Earlier this month chaos descended over El Paso, a city of about 700,000 roughly 50 miles (80km) from Fort Hancock, when the Federal Aviation Administration (FAA) abruptly ordered airspace to be shut down for 10 days only to lift the order eight hours later. The FAA cited “special security reasons” for the disruption, but it was later reveled that CBP had deployed a laser against what was thought to be a Mexican drug cartel drone but was in fact a party balloon.

The second incident in as many weeks occurred on Thursday when the military took action against what it said was a “seemingly threatening unmanned aerial system operating within military airspace”. The laser-based anti-drone system was activated, the Pentagon said, “far away from populated areas and there was no commercial aircraft in the vicinity”.

But top Democratic members of Congress who were briefed on the incident were livid about what they said was an ongoing lack of coordination within the Trump administration. US representatives Rick Larsen, Bennie Thompson and André Carson said that “our heads are exploding over the news”.

They accused the administration of “sidestepping” a bipartisan bill that would have improved training for drone operators and increased coordination between the FAA, the Pentagon and CBP. “Now we’re seeing the results of its incompetence,” the trio said.

The ranking Democratic member on the Senate aviation subcommittee, Tammy Duckworth from Illinois, has called for an independent investigation into both recent anti-drone incidents. “The Trump administration’s incompetence continues to cause chaos in our skies,” the senator said.

The airspace that has been closed is situated across the US-Mexico border from the valley of Juárez. The El Paso Times said that the area was renowned as a border smuggling corridor linked to the Sinaloa drug cartel.

The new restrictions on airspace around Fort Hancock will remain in place until 24 June, the FAA’s notice said.

There appeared to be ongoing disagreements between government agencies about how to handle the use of anti-drone lasers. The systems deploy high-powered laser beams to disable the machines.

The FAA is pressing for a safety review of the technology and wants all testing to be called off until that is completed. But Reuters is reporting that the Pentagon and CBP have indicated to congressional aides that they believe they can use the laser systems without having to consult the FAA in advance.