Charles Kinsey was wounded in the leg in the incident Monday in Miami, which came as he was trying to help a disoriented autistic man who had wandered away from a group home where Kinsey works as a therapist.
Police said they were responding to an emergency call about a man with a gun walking around and threatening suicide.
Cell phone footage shows Kinsey on the ground with his arms in the air, with the heavy-set young autistic man sitting on the ground nearby playing with a small white toy.
In the video, Kinsey can be heard shouting to police: "All he has is a toy truck. A toy truck. I am a behavioral therapist at a group home."
He was shot anyway. The video ends before that.
Kinsey was not seriously hurt.
The incident illustrates the edgy mood of US police and the nation in general after the police ambush in Dallas that left five officers dead and another similar incident Sunday in Baton Rouge, Louisiana that killed three.
Kinsey, 47, told Florida TV station WSVN-Channel 7 that as he lay on the ground he told police that he was unarmed.
"I am asking the officer, I said, 'sir, please don't shoot me. Please, do not shoot me.'"
Kinsey added: "It was like a mosquito bite, and when it hit me, I'm like, 'I still got my hands in the air, and I said, 'No I just got shot! And I'm saying, 'Sir, why did you shoot me?’ and his words to me, he said, 'I don't know.'"
The officer who opened fire has been placed on administrative leave for at least a week, the Miami Herald reported.
The investigation has been turned over to the Miami-Dade state attorney's office, it added.d