Indeed, the report said, only D.E.A. agents, not the Hondurans, had the necessary equipment to command the operation and had direct access to intelligence. Rather than taking orders from Honduran police, the agents gave “tactical commands” to the Hondurans during missions. Accounts of all three shootings, it said, showed that agency leaders “made the critical decisions and directed the actions taken during the mission.”

The D.E.A. refused to cooperate with the State Department as it sought to investigate what had happened in Ahuas. Michele M. Leonhart, then the agency’s administrator, told the inspector general she had approved that decision because subordinates told her there was no precedent for the State Department to investigate a D.E.A. shooting and it might compromise its investigations, the report said.

But the agency’s own review was “little more than a paper exercise” in which a FAST supervisor conducted no interviews and merely collected written statements from agents who omitted material facts, the report said.

The D.E.A. accepted the report’s observations and recommendations.

“The loss of life and injuries which occurred between May and July of 2012 were tragic,” Mary B. Schaefer, the agency’s chief compliance officer, wrote in a response. “D.E.A. acknowledges that its pre-mission preparation was not as thorough as it should have been and that the subsequent investigation lacked the depth and scope necessary to fully assess what transpired that night.”

Ms. Schaefer emphasized that the agency’s leadership had turned over since 2012 and that it had already made “significant changes in this area over the last five years.”

In particular, she disclosed, the agency “has disbanded its FAST program.” It had its last deployment in 2015 and was subsequently renamed. In March, its remaining personnel were folded into a program that trains agents for law-enforcement operations on domestic soil.