Police say he was resisting arrest
Pamerleau said the incident occurred after police responded to a domestic disturbance call coming from Flores' home Friday morning. When they arrived, they found a woman and baby, both of whom appeared to be injured.
Police say Flores then resisted arrest, and they tried to use nonlethal force -- stun guns and shields -- to subdue him, but those didn't work, Pamerleau said.
"Certainly what's in the video is a cause for concern," Pamerleau said. "But it's important to let the investigation go through its course so we can ensure a thorough and complete review of all that occurred."
She said both deputies fired shots after a "lengthy confrontation."
The Sheriff's Office identified the deputies as Greg Vasquez and Robert Sanchez. CNN attempted to reach out to them late Monday.
Vasquez and Sanchez have been with the Sheriff's Office for more than 10 years, according to Pamerleau. They have been placed on administrative leave.
The Bexar County District Attorney's Office has joined the investigation, according to KSAT.
Nicholas "Nico" LaHood, the Bexar County district attorney, told KSAT there's a second video of the incident that has a closer and clearer view of what happened.
"This is a very unique situation where we actually have the shooting on video," LaHood said. "That gives us a whole different perspective that we've never had to deal with before."
Flores had previous run-ins with the law. He was cited for possession of marijuana in 1995, criminal trespassing and aggravated assault in 1999, and aggravated robbery in 2003.
James Keith, media relations officer for the Bexar County Sheriff's Office, confirmed to CNN that his office has a second video of the shooting by someone else, but he would not go into detail about what it shows.
Dudes straight up didn't give a fukk. 
Dude only got $100 for that video?
