Chase Bishop, 29, turned himself into police and was booked into the Denver County jail on a single felony count, Denver District Attorney Beth McCann said in a statement.
The injured man, 24-year-old Tom Reddington, suffered a "serious, but not life-threatening" gunshot wound to his lower leg, McCann said.
Bishop was off-duty and was among revelers at the Mile High Spirits and Distillery nightclub in downtown Denver in the early morning hours of June 2, Denver police said in a statement.
A video of the incident captured by another bar patron, and spread widely online, showed Bishop break dancing, then performing a backflip. His handgun fell from his holster onto the dance floor and it discharged as Bishop picked it up. A muzzle flash can be seen on the video.
Bishop was going through the booking process late Tuesday afternoon, a jail spokeswoman said. It was unclear if he has retained legal counsel.
The FBI did not immediately respond to a request for comment.
After the shooting, Bishop was taken to Denver police headquarters but was released to his FBI supervisor.
Denver police spokesman Doug Schepman said in an email that once the investigation into the shooting is complete, the department will review the actions of its officers.
Mile High Spirits said on its Facebook page that the bar’s management was "deeply saddened" by the incident.
"It is shocking that the only shooting to ever occur at our establishment came about as a result of an FBI agent entering our distillery tasting room carrying a loaded firearm without our knowledge, in violation of our rules," the posting said.
The club offered the shooting victim "complimentary drinks for life."McCann said Bishop could face additional charges depending on test results of his blood-alcohol level.
Bishop is due in court for an advisement hearing on Wednesday. He faces a maximum 12 years in prison if convicted of the felony offense.
(Reporting by Keith Coffman; editing by Bill Tarrant and Leslie Adler)