The incident happened near the intersection of Broadway and Mollison at 2:10 p.m.
The involved officers were responding to a report of a man walking in traffic, El Cajon Police Department Chief Jeff Davis said at a news conference Tuesday night.
When officers arrived, the man, described as black and in his thirties, wearing a black tank top and blue jeans, refused multiple instructions by the first officer on the scene to “remove his concealed hand from in his pocket," according to a news release from police.
When the man did not comply, the officer drew his firearm and pointed at the man while continuing to instruct him to remove his hand from his pocket, according to the release.
A second officer then arrived. The man paced back and forth while the two officers tried to talk to him.
At one point, the man quickly pulled an object from his front pant pocket, placed both hands together on it, extended it towards the officer and took "what appeared to be a shooting stance,” Davis said.
One of the officers discharged his Taser. Simultaneously, an officer with a weapon discharged his weapon, striking the man, Davis said.
Officers provided first aid on scene until paramedics arrived and transported him to the hospital.
Davis said the object recovered from the scene was not a firearm.
A friend of the family of the man who was shot said the man's sister was the person who had called police for help, and that he struggled with mental issues.
Just after 3:30 p.m., El Cajon Police Department tweeted that officers responded to an "erratic subject that ended with an officer involved shooting."
The unnamed suspect was taken to Sharp Memorial Hospital, where he was initially listed in critical condition, according to El Cajon police.
The El Cajon Police Department has not yet been outfitted with body cameras.
A witness voluntarily handed a cell phone with video of the incident over to El Cajon police. Lt. Ransweiler said the video would be reviewed by investigators, including the San Diego County District Attorney's Office. Detectives were asking nearby businesses for surveillance video that may have captured the incident.
"I hope the community of El Cajon allows for the details of the investigation to be released," Ransweiler told reporters. "I'm confident that the community will support the decision made by the officer."
It was unknown how long it would take for authorities to release the video to the public, Lt. Ransweiler said. He pointed out that he believes it will eventually be released due to the District Attorney's new protocol.
San Diego City Councilwoman Myrtle Cole tweeted, "My heart goes out to the family & loved ones of the victim at the El Cajon shooting today. I pray that he survives."
A crowd of protesters that grew to about 100 people in the early evening arrived at the shopping center and later went to police headquarters. Many of them shouted angrily about what they characterized as a racially motivated police shooting and others took part in impromptu prayer circles.
Anyone with information about the incident was encouraged to contact the El Cajon Police Department.