The "all clear" was given after a report of an active shooter at Joint Base Andrews.
The base tweeted Thursday morning, instructing all personnel at the base in Washington's Maryland suburbs to shelter in place and says more information will be released as it comes.
But after conducting an investigation, officials determined there was no gunman, and the "all clear" was issued.
Officials now believe that during an active shooter drill, there were two personnel walking around with long guns and someone at the medical center looked out the window and saw that, NBC News reported. That person phoned in saying they saw "active shooters," meaning the two people carrying guns who were engaged in the active shooter drill and who were not shooting.
An employee at a medical facility at Joint Base Andrews outside Washington says an active-shooter drill had been planned, but officials later told workers it was a "real-world" situation.
Rodney Smith is a patient advocate at the military post's medical facility. He said Thursday that he was on lockdown and didn't have any more information.
Smith said by phone: "First it was an active-shooter exercise. Then it came back 'real world.'"
Smith said the situation was unfolding at the newer of two buildings at the Malcolm Grow Medical Facility on the base. He was in the older building.
Vice President Joe Biden was supposed to fly out of Join Base Andrews this morning to go to Ohio for an event for former Governor Ted Strickland at noon and a cancer event at 3 p.m., but he is now holding at the Naval Observatory.
Last month, Joint Base Andrews was placed on lockdown after a woman walked onto the base and claimed she had a bomb, NBC News reported.
An Explosive Ordinance Disposal team found the woman had no explosives, and she was apprehended.
— CNBC contributed to this report.