The moments before the shooting were recorded on cellphone video and show Charles Kinsey lying on the ground with his arms raised, talking to his patient and police throughout the standoff with officers, who appeared to have them surrounded.
"As long as I've got my hands up, they're not going to shoot me. This is what I'm thinking. They're not going to shoot me," he told WSVN-TV from his hospital bed, where he was recovering from a gunshot wound to his leg. "Wow, was I wrong."
The shooting comes amid weeks of violence involving police. Five officers were killed in Dallas two weeks ago and three law enforcement officers were gunned down Sunday in Baton Rouge, Louisiana. Before those shootings, a black man, Alton Sterling, 37, was fatally shot during a scuffle with two white officers at a convenience store.
At a news conference Thursday, North Miami Police Chief Gary Eugene said the investigation had been turned over to the Florida Department of Law Enforcement and the office of the state's attorney. He called it a "very sensitive matter" and promised a transparent investigation, but he refused to identify the officer or answer reporters' questions.
"I realize there are many questions about what happened on Monday night. You have questions, the community has questions, we as a city, we as a member of this police department and I also have questions," he said. "I assure you we will get all the answers."
The chief said officers responded following reports of a man with a gun threatening to kill himself, and the officers arrived "with that threat in mind" - but no gun was recovered.
Kinsey, 47, said he was trying to coax his 27-year-old patient back to a facility from which he had wandered. Police ordered Kinsey and the patient, who was sitting in the street playing with a toy truck, to lie on the ground.
"Lay down on your stomach," Kinsey says to his patient in the video, which was shot from a distance and provided to the Miami Herald on Wednesday. "Shut up!" responds the patient, who is sitting cross-legged in the road, playing with his toy.
"He has a toy truck in his hand! A toy truck!" Kinsey says to officers who have their guns drawn. Kinsey said he was more worried about his patient than himself.
An officer later fired three times, striking Kinsey in the leg, assistant police chief Neal Cuevas told the newspaper.
"I'm telling them again, 'Sir, there is no need for firearms. I'm unarmed, he's an autistic guy. He got a toy truck in his hand," Kinsey said.
"When he shot me, it was so surprising ... 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,'" Kinsey said.
After the shooting, Kinsey said he asked an officer why he was shot and the officer said "'I don't know.'"
Attorney General Loretta Lynch told reporters the Justice Department is aware of the shooting and working with local law enforcement to gather all of the facts and to decide how to proceed.
"We don't know enough about it at this point in time," she said, when asked whether federal authorities would begin their own investigation.
U.S. Rep. Frederica Wilson represents the area and said she was in shock after watching the video.
"From what I saw, he was lying on the ground with his hands up. Freezing. But he was still shot," she said.
"This is not typical of North Miami," she said. "We're not accustomed to this tension. ... This cannot happen again."
The officer has been placed on administrative leave, which is standard.
Kinsey's attorney, Hilton Napoleon, provided the cellphone video to the Herald.
In an interview with The Associated Press, he declined to say from whom he had obtained the video.
The video does not show the moment of the shooting, and Napoleon said there was about a two-minute gap in which the person who shot the video had switched off, thinking nothing more noteworthy would happen. It then briefly shows the aftermath of the shooting.