The US Navy's initial phase of investigation at Naval Medical Centre San Diego (NMCSD) could not establish a single witness report of gunshots at the basement of the hospital.
A statement issued by the US Navy read: "The intensive and thorough search of Building 26, as well as the grounds and additional buildings located on the grounds of NMCSD, did not reveal anything unusual after the initial witness report was made."
The investigation follows a witness reporting they heard three gunshots in the basement of Building 26, housing a gym, a barracks and an administrative facility located on the grounds of the Navy's Medical Center Balboa Park facility.
It triggered a lockdown of the medical facility and a 'shelter-in-place' order was imposed.
The San Diego Unified School District also reported closing two high schools and middle schools in the area as a precaution.
An immediate operation was launched by the police and K9 units garnering assistance from the US marshals, the Chula Vista Police Department, and the California Highway Patrol.
The Naval Base San Diego issued an alert to the facility through social media, and advised the non-emergency personnel to avoid the compound in the 34800 block of Bob Wilson Drive.
Reported by LA Times, the alert read: "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."
However, a thorough search could not track the gunman, neither were they able to detect any instances of shooting.
Following the initial investigation, the lockdown was lifted.
Further investigations are underway to verify what prompted issuing the alert of gunshots.
Earlier in 2012, a gunman shot 12 people dead and injured others at the Navy Yard installation in Washington.