The E4-B Boeing 747s, built in the 1970s during the Cold War, are essentially flying command centers that can refuel in the sky and are designed to remain airborne for days on end in times of crisis.
The Air Force has four E4-Bs, which also shuttle the secretary of defense around the world.
Two were damaged June 16 at Offutt Air Force Base, Nebraska when a tornado whipped through the area with little advance warning.
"Two E-4B National Airborne Operations Center aircraft stationed at Offutt AFB received storm damage," Air Force spokesman Colonel Pat Ryder said.
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Additionally, seven RC-135 reconnaissance planes suffered minor damage and another needed an inspection.
The E-4B is a 747 that has been reinforced to protect against the electromagnetic pulse from a nuclear blast and is shielded from a thermal blast.
"An advanced satellite communications system provides worldwide communication for senior leaders through the airborne operations center," the Air Force said.
The blue-and-white jets can also unspool miles of low-frequency antenna to maintain contact with nuclear subs and other assets in times of crisis.
