The incident happened Tuesday night at an apartment complex near Universal Studios in Orlando, Florida.
The agent, who was from Boston, was accompanied by other law enforcement officers when they raided the man's apartment.
A law enforcement official explained to ABC News that the man, who was an alleged "associate" of the Tsarnaev brothers, was cooperating with authorities when things suddenly escalated.
"There was some sort of aggressive movement that led the FBI agent to believe he was under threat and he opened fire," the law enforcement official said.
The dead man is identified as Ibragim Todashev.
The FBI issued a statement confirming that a shooting had taken place in the large Florida city, saying, "the agent encountered the suspect while conducting official duties... The suspect is deceased."
More information on the incident is expected to be released later today.