Base officials issued an all-clear message after about an hour for the base, where personnel had been told to shelter in place. A U.S. defense official said a second sweep was carried out at a medical facility out of "an abundance of caution."
"Fortunately, this was not a life-threatening situation," Colonel Brad Hoagland, 11th Wing and Joint Base Andrews commander, said in a statement. "We take all threats seriously and reacted to ensure the security of those on the base."
The military installation had been scheduled to hold a "no-notice" active shooter exercise late on Thursday morning, base officials said on Twitter.
But, the officials said, there was a "misidentification" of a security forces emergency services team that was conducting a routine inspection of the Malcolm Grow Medical Facility, on the opposite side of the base.
That led to reports of a "real-world" gunman at large at the hospital, the officials said. There had been no word of gunfire or casualties.
President Barack Obama, who flies out of Andrews on Air Force One, was not scheduled to use the base on Thursday. U.S. Vice President Joe Biden was scheduled to depart from Andrews during the morning for a trip to Ohio. He was holding at his official residence in Washington, his spokeswoman said during the lockdown.
The U.S. military has been on high alert for possible attacks at U.S. locations after incidents such as the July 2015 shooting rampage that killed five service members at two military offices in Chattanooga, Tennessee, and the 2009 shooting at a U.S. Army base in Fort Hood, Texas, in which a gunman killed 13 people.
The base in Maryland is the primary military air installation in the Washington, D.C., area, and is located about 15 miles (24 km) from the White House.
In May, Joint Base Andrews was put on lockdown after a woman claiming to have a bomb strapped to her chest arrived at the visitor center. The woman was apprehended and an explosives team determined there was no bomb.
Thursday's lockdown at Andrews revived memories of when a Coast Guard training drill in 2009 on the Potomac River in Washington sparked a brief security scare.
In that instance, the city was already on high alert because it was the anniversary of the Sept. 11, 2001, attacks on New York and Washington.