It provides a "highly survivable command, control and communications centre to direct United States forces, execute emergency war orders and coordinate actions by civil authorities", according to the Air Force.
The Air Force is still assessing the damage to the two Boeing 747s, Air Force spokesman Col.
The counting continues but officials say that according to preliminary estimates, Offutt Air Force Base is recovering from facility and infrastructure storm damages in the range of $7 million to $10 million.
The cost and timeline for repairing the two damaged E4-Bs is unknown. Initially, there were few details on the nature of the damage to the two E-4Bs.
"There is no impact to the E-4B's primary mission, so it remains capable of completing its National Airborne Operations Center", he said.
In addition, the tornado was damaged eight reconnaissance aircraft RC-135.
Eight 55th Wing aircraft received minor damage from the June 16 storm.
While not technically classified, the aircraft are rarely mentioned in the media.
In the event ground bases are destroyed, the "doomsday" plane acts as the command and control hub for the president, secretary of defense and joint chiefs.
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.
Aircraft fitted for similar purposes are in use by the Russian Air Force.