Military authorities are responding to a report of gunshots at a US naval medical centre.

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.

The navy hospital previously said on its Facebook page that an active shooter was reported and people were told to run, hide or fight.

Centre spokesman Mike Alvarez would not confirm there was an active shooter.

First responders and dog units are clearing the building.

The medical centre remains on lockdown and a shelter-in-place order has been given.

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.