Officials later said there was no sign of a shooting and no reports of deaths or injuries.
"There’s no evidence of a shooting right now that we know of, there was just a report of three shots heard," said Navy Region Southwest spokeswoman Amanda Chavez.
The U.S. Navy had said in an earlier statement, based on initial reports from a witness, that three shots were heard in the basement of a building housing a gym and barracks at the medical center around 8 a.m. PST (1600 GMT).
Military police were talking to the person who reported the shots fired, Chavez said.
First responders and Navy working dog units were on scene clearing the building where the shots were heard, the Navy statement said, adding that the medical center was on lockdown and a shelter-in-place order had been given.
Workers from the building were seen coming out in a single-file line with their hands raised in the air, as heavily armed police maintained a perimeter around the site.
The San Diego County Sheriff's Department sent an armored van and a roughly 12-officer SWAT team to assist military police in clearing the building, said sheriff's spokeswoman Jan Caldwell.
Navy Captain Curt Jones, asked about the status of the situation, said, "I would say we're pursuing the information we have and ensuring that everyone is safe."
A post on the medical center's Facebook page had earlier advised occupants to "run, hide or fight," the protocol advised by the U.S. Department of Homeland Security in response to an active shooter.
All non-emergency response staff were asked to stay away from the compound. The shooter was reported in building #26, the post said.
The medical center, about two miles (3 km) north of downtown San Diego, includes a 272-bed hospital and a staff of more than 6,500 military and civilian professionals, the center's website said.
A local middle school and two high schools in the area, which is home to the U.S. Navy's Pacific Fleet, were initially placed on lockdown as a precaution.