Employees became suspicious because something about the packages looked "out of place," said Jeff Bohn, a spokesman at Peterson Air Force Base in Colorado Springs, where the North American Aerospace Command is based.
Bohn declined to say what the packages looked like or what appeared to be amiss.
Tests performed on the packages ruled out chemical, biological and radiological agents, Bohn said. The packages were then removed and were undergoing other tests, he said.
Bohn said he did not know how the packages arrived or whether they had been screened before they were delivered. He said that would be part of the investigation.
NORAD is a joint U.S.-Canadian command that defends the skies over both nations and monitors sea approaches.
About 1,500 people were evacuated from the headquarters building.
NORAD's control room team was operating at a backup location inside Cheyenne Mountain because renovations were under way in the building on Peterson Air Force Base, said Navy Capt. Jeff Davis, a NORAD spokesman.
The Cheyenne Mountain site, carved out of the mountain in the 1960s to withstand a nuclear attack by the Soviet Union, used to be the primary control room.
In 2006, NORAD began preparations to move the control room to its current location on Peterson, saying it would save money and consolidate personnel. The Cheyenne Mountain control room is kept on standby for backup use.
NORAD shares its headquarters building with the U.S. Northern Command, which is responsible for defending U.S. territory from attack and helping civilian authorities.
Officials said essential Northern Command operations were not interrupted.