Earlier, the sprawling health facility, which employs more than 6,500 military, civilian, contractor and volunteer personnel, said on Facebook that there had been reports of an "active shooter."
"An active shooter has just been been reported in building #26 at Naval Medical Center San Diego. All occupants are advised to run, hide or fight. All non-emergency response personnel are asked to stay away from the compound," it posted.
The complex was "secured," the medical center later posted, adding that all children in childcare facilities at the medical center were "accounted for and safe." There were no injuries reported.
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Nearby elementary and middle schools, as well as Naval Base Point Loma, also in San Diego, were placed on precautionary lockdown, NBC affiliate KNSD reported.
Jones praised the response to the incident.
"We take all reports like this very seriously. We do a lot of training to help people recognize what they're supposed to do in the event of an active shooter," he said.
The sprawling facility employs more than 6,500 military, civilian, contractor and volunteer personnel.
Located about 2 1/2 miles from downtown San Diego, the 272-bed hospital has personnel who deploy to Iraq, Afghanistan, Kuwait, Djibouti and aboard the USNS Mercy, a Navy hospital ship.