Sheriff Alex Villanueva, whose department has been criticised during recent protests over racial injustice, expressed frustration over anti-police sentiment as he urged people to pray for the officers at a late-night news conference.
The department tweeted video of the shooting that shows a person open fire through the passenger-side window of the patrol vehicle. Authorities said on Twitter that demonstrators shouted "we hope they die".
Video of the incident showed a gunman in dark clothing approach the passenger's side window of the police auto and fire directly into the vehicle before running off, a shooting that the sheriff's department said was "without warning or provocation".
The suspect, who was seen in a security video taken from a nearby MTA camera, remains at large.
The Sheriff's Dept., says both deputies were shot multiple times and they are both undergoing surgery.
Donald Trump, who retweeted the video footage of the incident, described the shooter as an "animal", who needed to be "hit hard".
The Sheriff's Department also reports protesters blocks the hospital emergency entrances and exits while yelling "we hope they die".
Then he raised the pistol and fired several rounds inside of the vehicle, striking both deputies, Wegener said.
Following the shooting, the LASD reported on Twitter that protests took place outside of the hospital where the injured deputies were being treated.
Police later added: 'After deputies issued a dispersal order for the unlawful assembly of a group of protesters blocking the hospital emergency entrance & exits, a male adult protester refused to comply & cooperate...
KPCC/LAist reporter Josie Huang was arrested as she tried to document the deputies' arrest of one protester.
The deputies, who had graduated from the academy 14-months earlier, were able to radio for help. Turns out she was a member of the media, but at the time didn't identify herself or have proper press credentials, according the the Sheriff's Office.
"The gunman walked up on the deputies and opened fire without warning or provocation", the department stated.