The error triggered a military investigation, which found the codes were not compromised.
But the July 12 incident comes on the heels of a series of missteps by the Air Force that already had put the service under intense scrutiny.
Air Force officials said the deactivated codes were not at risk of being lost or stolen and that they were always contained at a secure facility.
The Air Force denies the base ever was locked down.
"This was just a procedural violation that we investigated," said Air Force Col. Dewey Ford, a spokesman at Patterson Air Force Base in Colorado. "We determined that there was no compromise."
The three crew members, who are in the 91st Missile Wing, were in the missile alert facility about 70 miles from Minot. That facility includes crew rest areas and sits above the underground control center where the actual keys can be turned to launch the ballistic missiles.There are no nuclear weapons on site.
"They were awaiting to get back to base and they fell asleep," Ford said.
It delivers another blow to the beleaguered Air Force.
"There are many reasons why procedures are in place to govern strict control of our nuclear arsenal. The new Air Force leadership, when confirmed, must take decisive and urgent steps to restore the culture of respect that our strategic weapons deserve and our national security demands. This trend is unacceptable," he said.
At the time, Gates said his decisions to sack the Air Force secretary and chief of staff were based mainly on the blistering conclusions of an internal report on the mistaken shipment to Taiwan of four Air Force fusing devices for ballistic missile nuclear warheads.
The investigation concluded that the codes had remained secured in their containers, which have combination locks that can only be opened by the crew. The containers remained with the crew at all times.