The Navy said Tuesday an initial inspection at Naval Medical Center San Diego found no sign of a gunman or a shooting.
The disclosure came after military police had checked Building 26 after a person reported hearing three shots in the basement earlier in the day, Navy spokesman N. Scott Sutherland said.
The base remained on lockdown as authorities went from room to room and led personnel out of the facility.
TV images showed uniformed Navy personnel walking outside the medical facility. Their hands were in the air and they were being patted down by base police as a precaution.
The Navy hospital previously said on its Facebook page that an active shooter was reported and people were told to "run, hide or fight."
All non-emergency personnel had been asked to stay away from the area.
A dozen unmarked SUVs - some with flashing lights - entered the center through the emergency room driveway gate around 9 a.m. A San Diego County Sheriff's Department armored truck followed minutes later.
Nearby Roosevelt Middle, and Garfield and San Diego High schools were placed on temporary lockdown as a precaution, CBS affiliate KFMB reported.
San Diego police Officer Travis Easter said police received a notification call from military police at 8:03 a.m. of shots fired but assistance was not requested.
Alvy Furlong, whose husband had surgery at the hospital last night, told KGTV-San Diego that a nurse came in and said to be prepared for possible evacuation.
"The doors are closed and locked," she said. "All of the windows have been covered."
Traffic backed up around the facility during the morning rush hour.
The 272-bed, multispecialty hospital and ambulatory complex is located on about 78 acres in the southeast corner of Balboa Park, about 2.5 miles from downtown, according to its website. Center staff is comprised of more than 6,500 military, civilian, contractor and volunteer personnel.
NMCSD personnel deploy to Iraq, Afghanistan, Kuwait, Djibouti and aboard the USNS Mercy, the website said. The facility is affiliated with 19 civilian nursing schools, training more than 400 students per year in clinical rotations.