NATO said the employee and family members had not visited its Supreme Headquarters Allied Powers Europe (SHAPE) facility in Mons, southern Belgium, since returning from Italy.
"There are three confirmed COVID-19 cases within our wider SHAPE community," NATO said in a statement.
"The cases were 'imported' to Belgium following foreign travel and the affected individuals have not entered the SHAPE site since returning home."
After testing at hospital, the three were sent home where they are in quarantine, but they are not said to be seriously ill.
SHAPE, the seat of NATO's military commander, US General Tod Wolters, counts some 5,000 people in its "community" - including military and civilian staff and their families.
As part of coronavirus precautions, travel by SHAPE officials has been restricted, with some meetings being held by phone or video conference rather than in person.
Visitor access to NATO's civilian headquarters in Brussels had already been limited, and military commanders given advice on preventing the spread of the virus.
The news came as the United States and Israel scrapped the remainder of their Juniper Cobra 20 joint military exercise due to the virus outbreak.
NATO has so far not cancelled any of the more than 20 exercises it has planned this year, but Secretary General Jens Stoltenberg said the alliance was closely monitoring the outbreak. "NATO military medical staff remain vigilant. They are monitoring any potential impact for NATO troops deployed on operations," an alliance official told AFP.