Investigators have found nothing to substantiate one person's report that someone fired gunshots Tuesday morning at the San Diego facility's Building 26, which contains barracks, a gym and administrative offices, Navy Capt. Curt Jones told reporters.
Authorities at the center's 78-acre campus ended a shelter-in-place order at 1:45 p.m., and patient care and access resumed thereafter, the Navy said.
An investigation "determined that no evidence could be found of shots fired and there were no casualties," the Navy said.
"The intensive and thorough search of Building 26, as well as the grounds and additional buildings on the grounds of NMCSD, did not reveal anything unusual after the initial witness report was made," the Navy said.
One witness reported hearing three gunshots in the basement of the building -- separate from the main hospital complex on campus -- about 8 a.m., Navy spokesman Kevin Dixon said.
That prompted a flurry of law enforcement activity, with military and local police searching the building as other officers took up positions nearby, directing pedestrians and cars away from the building in question.
The center, in its first Facebook post on the incident, said that "all occupants are advised to run, hide or fight."
After officers did a preliminary search, there were no reports of anyone injured, and there was no immediate evidence to suggest a gun had been fired, Jones said later in the morning.
Jones declined to say who had made the report, but characterized the person as "someone who thought they heard something and made reports."
Further information about what the person had seen or heard wasn't immediately available. Investigators were interviewing that person, a U.S. military official said.
Naval Medical Center San Diego bills itself as the largest military health care system in the Western United States. Situated on 78 acres surrounded by San Diego's Balboa Park, the center has a 272-bed hospital, eight clinics for active duty personnel and nine primary care sites for their family members.
The center had more than 1.2 million outpatient visits in 2014, admitting more than 19,000 patients that year. The hospital offers a comprehensive array of medical services, including births.
Video captured by CNN affiliate KUSI
showed people walking calmly from the area Tuesday morning.
Nearby restaurant Casa 1915 was keeping its doors closed as a precaution. The bistro was set to open at 10 a.m., but manager Keith Puryear said he decided to keep the business closed until the situation at the medical center ended.
Police didn't ask him to do that; it was a decision he made on his own.
"We're not terribly concerned at the moment," he said, "but we're exercising caution."
A middle school and two high schools in the vicinity were temporarily locked down as a precaution, the San Diego Unified School District said