The Drug Enforcement Administration has for five years steadfastly defended the behavior of its agents in a late-night drug seizure carried out with Honduran forces on the remote Mosquito Coast, a mission that resulted in the deaths of four Honduran civilians.

In the DEA’s view, the dead — one man, two women and a 14-year-old boy — were among those on a boat that shot at a canoe carrying a joint DEA-Honduran anti-drug team. The DEA said it had evidence in the form of night-vision video taken from a surveillance plane showing an “exchange of gunfire” between the two vessels after the larger boat collided with the canoe carrying the agents.

Now, for the first time, the three-hour video has been released to the public. It strongly suggests that the DEA’s account of crossfire in the May 2012 mission was not accurate. The release of the video, under a Freedom of Information Act request, follows a scathing report published by the inspectors general of the Departments of Justice and State earlier this year that challenged the DEA’s version of events.

The video shows numerous flashes of light consistent with gunshots originating from the anti-drug unit, according to Bruce Koenig, a forensic expert hired by ProPublica and The New York Times to analyze the images.

Mr. Koenig, who formerly was supervisor of the F.B.I.’s forensic audio/video group, examined the video frame by frame and concluded that only one flash originates from the passenger boat. In Mr. Koenig’s view, that flash could have been caused by a bullet striking the engine, which was later found to have a bullet hole. Infrared cameras detect heat and turn it into bright spots on video, so a muzzle flash from a gunshot and a spark from a bullet ricocheting off a metal surface can create similar flares.

The controversy over the agents’ actions has had an impact: As the DEA braced for the May release of the inspector general report on the episode, the agency disbanded the program that had run the interdiction operation, named the Foreign-Deployed Advisory Support Teams, or FAST. The FAST program provided military-style training to law enforcement officers in other countries to counter drug traffickers.

The inspectors general report, which found no evidence to support the DEA’s account that its agents were fired upon, has also drawn attention from lawmakers. A bipartisan group of four senators asserted that the DEA and State Department “repeatedly and knowingly misled members of Congress and congressional staff.”

“The DEA convinced themselves of a false version of events due to arrogance, false assumptions, and ignorance,” said Tim Rieser, an aide to Sen. Patrick Leahy and one of the staff members who has spent years delving into the shooting. “They rushed to judgment and then stuck to their story.”

Mary Brandenberger, a DEA spokeswoman, declined to comment on whether the agency still believed that an exchange of gunfire had taken place, because the episode was still under internal review. The agency has never retracted its view that the agents were fired upon and acted in self-defense.

For a crucial piece of evidence that it asserted would exonerate its personnel, the DEA kept the video under tight control. The first time it was shown outside the agency was in May 2012, shortly after the shooting, when it was screened in a secure conference room for a group of congressional staffers.

The DEA and State Department briefers controlled all the information, said Peter Quilter, a former staff member for the House Foreign Affairs Committee who attended some of initial briefings. “It was very difficult to second-guess them.” He added: “They very simply misled the Congress. The video did not back up their story of what happened.”

In at least eight briefings over six months, and in multiple letters in response to senators and representatives, the DEA maintained that the shooting was justified.

In June 2012, United States officials allowed a New York Times reporter to briefly view portions of the video, probably those shown to Congress. The officials pointed to blips in the grainy night-vision video, which they said were indications that the occupants of the passenger boat had fired on the team on the canoe. The Times described these flashes as less clearly visible than the ferocious series of shots from the canoe carrying the agents. The still-secret video was not definitive in supporting the DEA’s version of events, The Times reported, saying that the video “answers some questions while raising new ones” about the operation.

The video was released to the public through the Freedom of Information Act, with the law firm Jenner & Block taking on the case pro bono. A federal judge ordered the release of the video in January 2016, and the agency appealed. In June 2017, an appeals court ruled against the DEA, and the agency released the video.

The video opens on the outskirts of Ahuas, around 1 a.m. on May 11, 2012. A propeller plane touches down in a field and rolls to a stop. People gather around it and then carry dozens of blocky parcels to a nearby pickup truck. The parcels turned out to be more than 400 kilos of cocaine.

The cocaine is what brought the DEA to Ahuas, as part of a program called Operation Anvil. The DEA was working alongside the Honduran police and military to intercept drug shipments as they headed north.

In the video, the cocaine-filled pickup truck can be seen driving through the village to a landing on the twisting Patuca River. There the traffickers offload the drugs into a motorized canoe.

Four government helicopters appear and chaos erupts. The traffickers quickly abandon their task. One of them pushes the drug-laden canoe into the middle of the river and flees into the jungle with the others. Three members of the anti-drug team — two Honduran police and one DEA agent — ignore the men and pursue the canoe downstream.

The three men manage to climb on board. The DEA agent, sitting in the back, begins to pilot it back toward the landing. But the motor stalls and the canoe starts to drift downstream. The DEA agent can be seen vainly jerking the starter rope to try to restart the engine.

As he does this a second boat appears in the frame. It seems to be maneuvering directly toward the drifting canoe carrying the drugs. This second boat would turn out to be a water taxi, carrying a dozen passengers and cargo upriver to Ahuas.

The passengers and pilot on the civilian boat would later say they were terrified by the helicopters and did not intend to steer toward the canoe containing the law enforcement agents. For their part, the drug agents assumed the second boat was trying to recover the drugs.

It remains unclear why the civilian craft steered directly into the boat with the agents, but the boats collided.

The video clearly shows gunfire from the anti-drug agents. As passengers leap into the water, the anti-drug team continues to fire at them. An eight-second burst of machine gun fire comes from one of the helicopters. (The inspectors general report said a DEA agent ordered a Honduran door gunner to fire.)

The footage cuts away for a moment, and the edges of the video are blocked by DEA redactions, obscuring the surveillance plane’s altitude and other technical intelligence-gathering data the agency deemed sensitive.

While it is impossible to determine what is happening off camera, or underneath the blurred areas, any gunfire originating from the passenger boat — the evidence at the heart of the case that DEA officials made to Congress — is strikingly difficult to discern.

In the end, four passengers were killed and three were injured.

In the months after the shooting, the DEA struggled to produce evidence that someone on the passenger boat had been armed. No bullets had struck the helicopters, the agents or their canoe.

The Ahuas killings were among three fatal shooting cases that took place during Operation Anvil. The inspectors general found that the other two cases were also followed by inaccurate reports from the field. In one, they concluded, a Honduran police officer planted a gun on the dead body of an unarmed drug trafficker.

Carson Ulrich, who served as deputy for the FAST team missions at the time of the Ahuas shooting, stands by the DEA’s assertions that the passenger boat was searching for the drugs and had fired on the anti-drug team.

Mr. Ulrich argued that the now-disbanded FAST program was “desperately” needed to “bring the rule of law to an area governed by the cartels.” The United States inspectors general were biased, Ulrich contended. “They are slandering heroes. I dare anyone to pick up a rifle and do what these American agents did.”

When reached by phone, Hilda Lezama, who operated the passenger boat with her husband, said that she still suffered from “extreme pain” from bullet wounds in both of her legs, and is no longer able to work. “I can’t afford to support my daughters,” she said. “We still don’t know why this happened.”