Update: 6.05pm: SWAT teams are conducting floor-by- floor searches of the naval hospital.
So far they have not encountered signs of a shooting or anyone who has been wounded.
Police in San Diego say only one witness has called them about it in the last couple of hours, but they are still treating it as an "active situation".
A navy spokesman said the report of three gunshots heard at the Naval Medical Centre San Diego (NMCSD) came from a single witness.
The shots were reportedly heard in the basement of the centre’s Building 26, navy region southwest spokesman Scott Sutherland said.
Earlier: Military authorities are responding to reported gunshots at a building on the campus of the Naval Medical Centre San Diego.
The sounds were heard at around 8am local time in Building 26, spokesman Mike Alvarez said.
The building houses offices and barracks for wounded sailors and marines as well as a gym.
Mr Alvarez said all non-emergency personnel have been asked to stay away from the area.
A post on the Facebook page of the Naval Medical Centre in San Diego is advising people there to "run, hide or fight".
Click here if you can't see the Facebook post above.
The 272-bed, multi-specialty hospital and ambulatory complex is located on about 78 acres in the south-east corner of Balboa Park, about 2.5 miles from the city centre, according to its website.
Centre staff include more than 6,500 military, civilian, contractor and volunteer personnel.
NMCSD personnel deploy to Iraq, Afghanistan, Kuwait, Djibouti and aboard the USNS Mercy ship, the website said.