The Federal Aviation Administration on Friday gave the military the green light to use high-energy lasers to shoot down suspected drones in U.S. airspace, ending a two-month standoff over whether the weapons endangered airplanes.

Bryan Bedford, the F.A.A. administrator, said in a statement that the F.A.A. had completed a safety assessment of the anti-drone systems used by the military and had “determined that these systems do not present an increased risk to the flying public.”

The decision was a striking about-face for the F.A.A., which twice shut down swaths of airspace over the Texas border with Mexico in February after the lasers were deployed without the agency’s approval.

The statement did not address whether the agency had determined that the high-energy lasers posed no physical risk to aircraft, or whether the safety determination was based on how the lasers were being deployed. But the F.A.A. determined that the risk would be minimal even if the laser came into contact with an airplane, according to an agency official who spoke on the condition of anonymity to discuss a sensitive matter.

The F.A.A. is expected to issue an advisory to pilots operating in the vicinity of the southern border to be aware of increased anti-drone laser use in the area, according to a transportation official.

The F.A.A.’s decision allows the Pentagon and other agencies to use the high-energy lasers liberally along the southern border, where they have emerged as a key tool in the Trump administration’s efforts to take out drones used by drug cartels based in Mexico and elsewhere.

It was not clear if the agreement, announced jointly with the Defense Department, would quiet concerns among lawmakers that the F.A.A. was being pressured into approving the Pentagon’s plans to use the lasers. Senator Maria Cantwell of Washington, the top Democrat on the committee that oversees aviation, has requested a briefing from the Pentagon and F.A.A. about what led to the agreement, an aide said.