The attack at the Islamic Centre of San Diego is being investigated as a hate crime, San Diego Police chief Scott Wahl said at a news conference at a neighbourhood park near the mosque.
He said the “circumstances that led up to this” would come out in the days ahead.
Among those killed was a mosque security guard, who police believe “played a pivotal role” in keeping the attack from being “much worse”, Mr Wahl said.
Police on a roof at the scene of the shooting in San Diego (Gregory Bull/AP)
The centre is the largest mosque in San Diego County and includes the Al Rashid School that offers courses in Arabic language, Islamic studies and the Koran for students aged five and over, according to its website.
“All of the kids are safe,” Mr Wahl said, appearing emotional. “Our hearts go out to the families that are in this moment being notified of what has happened to their loved ones.”
Police responded within four minutes of being called, Mr Wahl said. As they arrived, gunshots rang out a few blocks away where a landscaper was shot at but uninjured. The gunmen were found dead in a vehicle stopped in the middle of a road nearby, he said.
Aerial TV footage showed more than a dozen children holding hands and being walked out of the car park of the centre as it was surrounded by scores of police vehicles. The white mosque is in a neighbourhood of homes, apartments and shopping centres with Middle Eastern restaurants and markets.
Parents were directed to a nearby area to retrieve their children.
A crowd gathers near the scene of the shooting in San Diego (Gregory Bull/AP)
The mosque’s director, Imam Taha Hassane, called it “extremely outrageous to target a place of worship”.
“All the places of worship in our beautiful city should always be protected,” he said.
He added that the centre focused on interfaith relations and community building, and that a group of non-Muslims had been touring the mosque earlier on Monday to learn about Islam.
The Islamic centre’s website says its mission is to not only serve the Muslim population but also “work with the larger community to serve the less fortunate, to educate, and to better our nation”.
Five daily prayers are held there, and the mosque works with other organisations and people of all faiths on social causes.
The Council on American-Islamic Relations, one of the largest Muslim civil rights and advocacy groups in the US, condemned the shooting.