Officers said they used a Taser and opened fire after the man failed to follow their commands and appeared to pull an object out of his pocket, holding it in an apparent shooting stance, KMFB reported.
At a news conference late Tuesday, police confirmed that "no firearm was recovered" from the scene, according to KMFB. KSWB reports that a witness said the man was unarmed and mentally ill.
>> PHOTOS: Protests after El Cajon, California, police shooting
KMFB initially reported that the man was critically injured and taken to the hospital, although the woman who identified herself as the man's sister said he died at the scene. Police said late Tuesday that the man was dead, KMFB tweeted.
Here's what we know so far:
1. Some bystanders said the man had his hands up. While describing the incident to KNSD, witness Michael Ray Rodriguez said, "The man's hands are up. No shirt. He didn't have no shirt."
El Cajon police denied those claims in a tweet Tuesday night, saying that in "video voluntarily provided by a witness, the subject did NOT have his hands up in the air."
2. A now-viral Facebook Live video captured the aftermath of the shooting. In the 25-minute video, posted by Rumbie Mubaiwa, a woman cries that she had called police to help the man, who she said was her brother.
"I just called for help, and you came and killed him," she says.
She later asks, "Don't you guys have crisis communications teams to talk to somebody mentally sick?"
The video has been viewed more than 33,000 times.
>> Watch the video here (WARNING: Graphic content and language)
3. Police have denied claims that officers confiscated cellphones from people at a nearby restaurant. A woman identified only as Maria told KNSD that police took cellphones from employees at Los Panchos restaurant and told workers "not to talk to anyone."
El Cajon police tweeted, "We ask that the community please be careful about reacting to inaccurate information. No phones were confiscated from anyone at the scene."
During the Tuesday night news conference, Police Chief Jeff Davis said a witness voluntarily handed cellphone video over to police.
"That witness voluntarily provided their phone to the police department and gave written consent for the officers to view the video," the department said in a press release. "Investigators have been able to download the video. This was the only phone provided to officers in this investigation."
4. The officers involved are being placed on administrative leave. According to KMFB, that includes the officer who fired at the man and the one who used a Taser. Each officer has at least 20 years of police service, KMFB reported.
5. El Cajon police do not yet wear body cameras. KNSD reported that the City Council recently approved a plan to buy body cameras, but Davis said they likely won't be used until next year.