The Navy says an initial inspection at the medical center found no sign of a gunman or a shooting.
Military authorities responded Tuesday to a report of gunshots at a building on the campus Naval Medical Center San Diego.
The hospital posted on its Facebook page: "An active shooter has just been reported in building #26 at Naval Medical Center San Diego. All occupants are advised to run, hide or fight."
Spokesman Mike Alvarez said, however, that "I cannot confirm an active shooter."
The sounds were heard around 8 a.m. in Building 26, which houses offices and barracks for wounded sailors and Marines as well as a gym, said spokesman Mike Alvarez.
All non-emergency personnel were asked to stay away from the area.
He said at least three gunshots were reported heard.
"We're not taking any chances and are executing procedures we've been trained for in this kind of situation," Alvarez said.
San Diego police Officer Travis Easter said police received a notification call from military police at 8:03 a.m. of shots fired but assistance was not requested.
Traffic backed up around the facility during the morning rush hour.
The 272-bed, multispecialty hospital and ambulatory complex is located on about 78 acres in the southeast corner of Balboa Park, about 2.5 miles from downtown, according to its website. Center staff is comprised of more than 6,500 military, civilian, contractor and volunteer personnel.
NMCSD personnel deploy to Iraq, Afghanistan, Kuwait, Djibouti and aboard the USNS Mercy, the website said. The facility is affiliated with 19 civilian nursing schools, training more than 400 students per year in clinical rotations.