Cars enter Naval Base San Diego on May 8, 2015 in San Diego, California. PHOTO: AFP
Navy spokesperson Jon Nylander told AFP that a single witness had reported hearing three shots in the basement of the building at about 8:00 am (1500 GMT).
Local police, assisted by Navy dogs and California Highway Patrol officers, searched the building but there were no immediate signs of a shooting or reports of casualties.
"They did an initial sweep and they didn't find anything, so they are doing a more thorough sweep," Nylander said.
"They have not located any evidence of a shooting having taken place."
Authorities rushed to the hospital following the report of gunfire. The facility posted a message on Facebook warning people of the possible shooting.
"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," the hospital posted on its official Facebook page.
The nearby Naval Base San Diego also posted information online about a possible shooting.
San Diego, the southernmost city on the California coast, has a sprawling military infrastructure and is a major port for the US Navy.
The hospital is located in the city's Balboa Park, close to San Diego's famous zoo.
The United States has seen several deadly shootings at military installations in recent years.
In November 2009, US Army psychiatrist Major Nidal Hasan opened fire at his Texas military base, Fort Hood. He killed 13 people and wounded more than 30 more, before being overpowered by police.
In September 2013, Aaron Alexis killed 12 people and wounded eight others at the Washington Navy Yard, just two miles (three kilometers) from the US Capitol building, before he was shot dead by officers.
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